PDB Short entry for 2Z1Z HEADER TRANSFERASE 16-MAY-07 2Z1Z TITLE CRYSTAL STRUCTURE OF LL-DIAMINOPIMELATE AMINOTRANSFERASE FROM TITLE 2 ARABIDOPSIS THALIANA COMPLEXED WITH L-MALATE ION COMPND MOL_ID: 1; COMPND 2 MOLECULE: LL-DIAMINOPIMELATE AMINOTRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: HYPOTHETICAL PROTEIN AT4G33680, HYPOTHETICAL PROTEIN COMPND 5 T16L1.170; COMPND 6 EC: 2.6.1.83; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: THALE CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: AT4G33680; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: M15(PREP4); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PQE60 KEYWDS LL-DIAMINOPIMELATE AMINOTRANSFERASE, LL-DAP-AT, PLP, ARABIDOPSIS KEYWDS 2 THALIANA, LYSINE BIOSYNTHESIS, THDPA, LL-DAP, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR N.WATANABE,M.M.CHERNEY,M.J.VAN BELKUM,S.L.MARCUS,M.D.FLEGEL,M.D.CLAY, AUTHOR 2 M.K.DEYHOLOS,J.C.VEDERAS,M.N.G.JAMES REVDAT 5 03-APR-24 2Z1Z 1 REMARK SEQADV LINK REVDAT 4 13-JUL-11 2Z1Z 1 VERSN REVDAT 3 24-FEB-09 2Z1Z 1 VERSN REVDAT 2 09-OCT-07 2Z1Z 1 JRNL REVDAT 1 17-JUL-07 2Z1Z 0 JRNL AUTH N.WATANABE,M.M.CHERNEY,M.J.VAN BELKUM,S.L.MARCUS,M.D.FLEGEL, JRNL AUTH 2 M.D.CLAY,M.K.DEYHOLOS,J.C.VEDERAS,M.N.JAMES JRNL TITL CRYSTAL STRUCTURE OF LL-DIAMINOPIMELATE AMINOTRANSFERASE JRNL TITL 2 FROM ARABIDOPSIS THALIANA: A RECENTLY DISCOVERED ENZYME IN JRNL TITL 3 THE BIOSYNTHESIS OF L-LYSINE BY PLANTS AND CHLAMYDIA JRNL REF J.MOL.BIOL. V. 371 685 2007 JRNL REFN ISSN 0022-2836 JRNL PMID 17583737 JRNL DOI 10.1016/J.JMB.2007.05.061 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.2 REMARK 3 NUMBER OF REFLECTIONS : 35896 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1916 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2616 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.85 REMARK 3 BIN R VALUE (WORKING SET) : 0.2440 REMARK 3 BIN FREE R VALUE SET COUNT : 154 REMARK 3 BIN FREE R VALUE : 0.3170 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6288 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 39 REMARK 3 SOLVENT ATOMS : 223 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.57 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.16000 REMARK 3 B22 (A**2) : -1.16000 REMARK 3 B33 (A**2) : 1.73000 REMARK 3 B12 (A**2) : -0.58000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.373 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.271 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.180 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.699 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.905 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6476 ; 0.028 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8778 ; 2.374 ; 1.957 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 814 ; 8.548 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 286 ;36.465 ;24.056 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1032 ;21.136 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 32 ;21.553 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 945 ; 0.173 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4984 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 3112 ; 0.245 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4351 ; 0.318 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 322 ; 0.176 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 45 ; 0.233 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 10 ; 0.271 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 4176 ; 1.259 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6500 ; 2.080 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2689 ; 3.330 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2278 ; 4.824 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2Z1Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-MAY-07. REMARK 100 THE DEPOSITION ID IS D_1000027419. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-OCT-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.11590 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : KOHZU: DOUBLE CRYSTAL SI(111) REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37831 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.4 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08300 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.55300 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NATIVE LL-DIAMINOPIMELATE AMINOTRANSFERASE REMARK 200 STRUCTURE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.1M D,L-MALIC ACID, PH7.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 115.29267 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 57.64633 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 57.64633 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 115.29267 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 9100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -45.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 LYS A 3 REMARK 465 ARG A 4 REMARK 465 VAL A 5 REMARK 465 ASN A 6 REMARK 465 THR A 7 REMARK 465 CYS A 8 REMARK 465 LYS A 9 REMARK 465 CYS A 10 REMARK 465 VAL A 11 REMARK 465 ALA A 12 REMARK 465 THR A 13 REMARK 465 PRO A 14 REMARK 465 GLN A 15 REMARK 465 GLU A 16 REMARK 465 LYS A 17 REMARK 465 ILE A 18 REMARK 465 HIS A 427 REMARK 465 HIS A 428 REMARK 465 HIS A 429 REMARK 465 HIS A 430 REMARK 465 HIS A 431 REMARK 465 HIS A 432 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 LYS B 3 REMARK 465 ARG B 4 REMARK 465 VAL B 5 REMARK 465 ASN B 6 REMARK 465 THR B 7 REMARK 465 CYS B 8 REMARK 465 LYS B 9 REMARK 465 CYS B 10 REMARK 465 VAL B 11 REMARK 465 ALA B 12 REMARK 465 THR B 13 REMARK 465 PRO B 14 REMARK 465 GLN B 15 REMARK 465 GLU B 16 REMARK 465 LYS B 17 REMARK 465 ILE B 18 REMARK 465 HIS B 427 REMARK 465 HIS B 428 REMARK 465 HIS B 429 REMARK 465 HIS B 430 REMARK 465 HIS B 431 REMARK 465 HIS B 432 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 CYS A 130 CB CYS A 130 SG 0.109 REMARK 500 GLU A 218 CG GLU A 218 CD 0.098 REMARK 500 TYR A 271 CE1 TYR A 271 CZ 0.093 REMARK 500 GLU B 218 CB GLU B 218 CG 0.152 REMARK 500 GLU B 218 CG GLU B 218 CD 0.108 REMARK 500 GLU B 225 CG GLU B 225 CD 0.106 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 45 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ASP A 149 CB - CG - OD1 ANGL. DEV. = 6.4 DEGREES REMARK 500 ASP A 149 CB - CG - OD2 ANGL. DEV. = -5.6 DEGREES REMARK 500 LEU A 193 CB - CG - CD1 ANGL. DEV. = -12.0 DEGREES REMARK 500 TYR A 271 CA - CB - CG ANGL. DEV. = 11.7 DEGREES REMARK 500 ARG A 278 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 PRO A 363 C - N - CA ANGL. DEV. = 9.3 DEGREES REMARK 500 GLY A 398 N - CA - C ANGL. DEV. = 18.5 DEGREES REMARK 500 ARG A 404 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 420 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG A 420 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 GLY B 36 N - CA - C ANGL. DEV. = -18.9 DEGREES REMARK 500 ARG B 45 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 ARG B 45 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 CYS B 205 CA - CB - SG ANGL. DEV. = 7.6 DEGREES REMARK 500 ASP B 237 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 VAL B 365 CB - CA - C ANGL. DEV. = 12.1 DEGREES REMARK 500 GLY B 398 N - CA - C ANGL. DEV. = 15.7 DEGREES REMARK 500 ARG B 420 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 SER A 92 -64.43 -105.37 REMARK 500 ALA A 96 124.79 -37.75 REMARK 500 ASN A 177 16.41 86.00 REMARK 500 PHE A 274 31.36 -78.17 REMARK 500 ARG A 278 87.57 85.51 REMARK 500 PRO A 363 31.57 -77.25 REMARK 500 ASN B 27 109.44 -44.09 REMARK 500 LEU B 33 -165.59 -59.81 REMARK 500 GLN B 34 158.38 172.85 REMARK 500 ALA B 35 54.19 32.65 REMARK 500 TYR B 37 126.62 108.74 REMARK 500 ILE B 63 121.69 -33.40 REMARK 500 GLU B 89 -74.36 -39.35 REMARK 500 SER B 92 -96.30 -102.79 REMARK 500 ALA B 96 73.64 59.38 REMARK 500 ASN B 177 2.28 87.63 REMARK 500 VAL B 261 -1.82 -140.31 REMARK 500 PHE B 274 12.76 -69.29 REMARK 500 ARG B 278 85.93 85.91 REMARK 500 ALA B 311 153.30 -44.02 REMARK 500 SER B 351 -8.90 -57.00 REMARK 500 THR B 389 -163.32 -113.68 REMARK 500 GLN B 423 -71.14 -28.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 398 GLY A 399 36.05 REMARK 500 GLU A 400 GLY A 401 -41.52 REMARK 500 TYR A 425 LYS A 426 -147.29 REMARK 500 TYR B 94 GLY B 95 123.88 REMARK 500 GLY B 95 ALA B 96 -131.02 REMARK 500 GLY B 398 GLY B 399 52.76 REMARK 500 TYR B 425 LYS B 426 -131.82 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 PLP A 500 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MLT A 433 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PLP A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PLP B 501 DBREF 2Z1Z A 1 426 UNP O81885 O81885_ARATH 1 426 DBREF 2Z1Z B 1 426 UNP O81885 O81885_ARATH 1 426 SEQADV 2Z1Z HIS A 427 UNP O81885 EXPRESSION TAG SEQADV 2Z1Z HIS A 428 UNP O81885 EXPRESSION TAG SEQADV 2Z1Z HIS A 429 UNP O81885 EXPRESSION TAG SEQADV 2Z1Z HIS A 430 UNP O81885 EXPRESSION TAG SEQADV 2Z1Z HIS A 431 UNP O81885 EXPRESSION TAG SEQADV 2Z1Z HIS A 432 UNP O81885 EXPRESSION TAG SEQADV 2Z1Z HIS B 427 UNP O81885 EXPRESSION TAG SEQADV 2Z1Z HIS B 428 UNP O81885 EXPRESSION TAG SEQADV 2Z1Z HIS B 429 UNP O81885 EXPRESSION TAG SEQADV 2Z1Z HIS B 430 UNP O81885 EXPRESSION TAG SEQADV 2Z1Z HIS B 431 UNP O81885 EXPRESSION TAG SEQADV 2Z1Z HIS B 432 UNP O81885 EXPRESSION TAG SEQRES 1 A 432 MET ALA LYS ARG VAL ASN THR CYS LYS CYS VAL ALA THR SEQRES 2 A 432 PRO GLN GLU LYS ILE GLU TYR LYS THR LYS VAL SER ARG SEQRES 3 A 432 ASN SER ASN MET SER LYS LEU GLN ALA GLY TYR LEU PHE SEQRES 4 A 432 PRO GLU ILE ALA ARG ARG ARG SER ALA HIS LEU LEU LYS SEQRES 5 A 432 TYR PRO ASP ALA GLN VAL ILE SER LEU GLY ILE GLY ASP SEQRES 6 A 432 THR THR GLU PRO ILE PRO GLU VAL ILE THR SER ALA MET SEQRES 7 A 432 ALA LYS LYS ALA HIS GLU LEU SER THR ILE GLU GLY TYR SEQRES 8 A 432 SER GLY TYR GLY ALA GLU GLN GLY ALA LYS PRO LEU ARG SEQRES 9 A 432 ALA ALA ILE ALA LYS THR PHE TYR GLY GLY LEU GLY ILE SEQRES 10 A 432 GLY ASP ASP ASP VAL PHE VAL SER ASP GLY ALA LYS CYS SEQRES 11 A 432 ASP ILE SER ARG LEU GLN VAL MET PHE GLY SER ASN VAL SEQRES 12 A 432 THR ILE ALA VAL GLN ASP PRO SER TYR PRO ALA TYR VAL SEQRES 13 A 432 ASP SER SER VAL ILE MET GLY GLN THR GLY GLN PHE ASN SEQRES 14 A 432 THR ASP VAL GLN LYS TYR GLY ASN ILE GLU TYR MET ARG SEQRES 15 A 432 CYS THR PRO GLU ASN GLY PHE PHE PRO ASP LEU SER THR SEQRES 16 A 432 VAL GLY ARG THR ASP ILE ILE PHE PHE CYS SER PRO ASN SEQRES 17 A 432 ASN PRO THR GLY ALA ALA ALA THR ARG GLU GLN LEU THR SEQRES 18 A 432 GLN LEU VAL GLU PHE ALA LYS LYS ASN GLY SER ILE ILE SEQRES 19 A 432 VAL TYR ASP SER ALA TYR ALA MET TYR MET SER ASP ASP SEQRES 20 A 432 ASN PRO ARG SER ILE PHE GLU ILE PRO GLY ALA GLU GLU SEQRES 21 A 432 VAL ALA MET GLU THR ALA SER PHE SER LYS TYR ALA GLY SEQRES 22 A 432 PHE THR GLY VAL ARG LEU GLY TRP THR VAL ILE PRO LYS SEQRES 23 A 432 LYS LEU LEU TYR SER ASP GLY PHE PRO VAL ALA LYS ASP SEQRES 24 A 432 PHE ASN ARG ILE ILE CYS THR CYS PHE ASN GLY ALA SER SEQRES 25 A 432 ASN ILE SER GLN ALA GLY ALA LEU ALA CYS LEU THR PRO SEQRES 26 A 432 GLU GLY LEU GLU ALA MET HIS LYS VAL ILE GLY PHE TYR SEQRES 27 A 432 LYS GLU ASN THR ASN ILE ILE ILE ASP THR PHE THR SER SEQRES 28 A 432 LEU GLY TYR ASP VAL TYR GLY GLY LYS ASN ALA PRO TYR SEQRES 29 A 432 VAL TRP VAL HIS PHE PRO ASN GLN SER SER TRP ASP VAL SEQRES 30 A 432 PHE ALA GLU ILE LEU GLU LYS THR HIS VAL VAL THR THR SEQRES 31 A 432 PRO GLY SER GLY PHE GLY PRO GLY GLY GLU GLY PHE VAL SEQRES 32 A 432 ARG VAL SER ALA PHE GLY HIS ARG GLU ASN ILE LEU GLU SEQRES 33 A 432 ALA CYS ARG ARG PHE LYS GLN LEU TYR LYS HIS HIS HIS SEQRES 34 A 432 HIS HIS HIS SEQRES 1 B 432 MET ALA LYS ARG VAL ASN THR CYS LYS CYS VAL ALA THR SEQRES 2 B 432 PRO GLN GLU LYS ILE GLU TYR LYS THR LYS VAL SER ARG SEQRES 3 B 432 ASN SER ASN MET SER LYS LEU GLN ALA GLY TYR LEU PHE SEQRES 4 B 432 PRO GLU ILE ALA ARG ARG ARG SER ALA HIS LEU LEU LYS SEQRES 5 B 432 TYR PRO ASP ALA GLN VAL ILE SER LEU GLY ILE GLY ASP SEQRES 6 B 432 THR THR GLU PRO ILE PRO GLU VAL ILE THR SER ALA MET SEQRES 7 B 432 ALA LYS LYS ALA HIS GLU LEU SER THR ILE GLU GLY TYR SEQRES 8 B 432 SER GLY TYR GLY ALA GLU GLN GLY ALA LYS PRO LEU ARG SEQRES 9 B 432 ALA ALA ILE ALA LYS THR PHE TYR GLY GLY LEU GLY ILE SEQRES 10 B 432 GLY ASP ASP ASP VAL PHE VAL SER ASP GLY ALA LYS CYS SEQRES 11 B 432 ASP ILE SER ARG LEU GLN VAL MET PHE GLY SER ASN VAL SEQRES 12 B 432 THR ILE ALA VAL GLN ASP PRO SER TYR PRO ALA TYR VAL SEQRES 13 B 432 ASP SER SER VAL ILE MET GLY GLN THR GLY GLN PHE ASN SEQRES 14 B 432 THR ASP VAL GLN LYS TYR GLY ASN ILE GLU TYR MET ARG SEQRES 15 B 432 CYS THR PRO GLU ASN GLY PHE PHE PRO ASP LEU SER THR SEQRES 16 B 432 VAL GLY ARG THR ASP ILE ILE PHE PHE CYS SER PRO ASN SEQRES 17 B 432 ASN PRO THR GLY ALA ALA ALA THR ARG GLU GLN LEU THR SEQRES 18 B 432 GLN LEU VAL GLU PHE ALA LYS LYS ASN GLY SER ILE ILE SEQRES 19 B 432 VAL TYR ASP SER ALA TYR ALA MET TYR MET SER ASP ASP SEQRES 20 B 432 ASN PRO ARG SER ILE PHE GLU ILE PRO GLY ALA GLU GLU SEQRES 21 B 432 VAL ALA MET GLU THR ALA SER PHE SER LYS TYR ALA GLY SEQRES 22 B 432 PHE THR GLY VAL ARG LEU GLY TRP THR VAL ILE PRO LYS SEQRES 23 B 432 LYS LEU LEU TYR SER ASP GLY PHE PRO VAL ALA LYS ASP SEQRES 24 B 432 PHE ASN ARG ILE ILE CYS THR CYS PHE ASN GLY ALA SER SEQRES 25 B 432 ASN ILE SER GLN ALA GLY ALA LEU ALA CYS LEU THR PRO SEQRES 26 B 432 GLU GLY LEU GLU ALA MET HIS LYS VAL ILE GLY PHE TYR SEQRES 27 B 432 LYS GLU ASN THR ASN ILE ILE ILE ASP THR PHE THR SER SEQRES 28 B 432 LEU GLY TYR ASP VAL TYR GLY GLY LYS ASN ALA PRO TYR SEQRES 29 B 432 VAL TRP VAL HIS PHE PRO ASN GLN SER SER TRP ASP VAL SEQRES 30 B 432 PHE ALA GLU ILE LEU GLU LYS THR HIS VAL VAL THR THR SEQRES 31 B 432 PRO GLY SER GLY PHE GLY PRO GLY GLY GLU GLY PHE VAL SEQRES 32 B 432 ARG VAL SER ALA PHE GLY HIS ARG GLU ASN ILE LEU GLU SEQRES 33 B 432 ALA CYS ARG ARG PHE LYS GLN LEU TYR LYS HIS HIS HIS SEQRES 34 B 432 HIS HIS HIS HET MLT A 433 9 HET PLP A 500 15 HET PLP B 501 15 HETNAM MLT D-MALATE HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETSYN MLT (2R)-2-HYDROXYBUTANEDIOIC ACID; 2-HYDROXY-SUCCINIC ACID HETSYN PLP VITAMIN B6 PHOSPHATE FORMUL 3 MLT C4 H6 O5 FORMUL 4 PLP 2(C8 H10 N O6 P) FORMUL 6 HOH *223(H2 O) HELIX 1 1 ASN A 27 LEU A 33 1 7 HELIX 2 2 TYR A 37 TYR A 53 1 17 HELIX 3 3 PRO A 71 LEU A 85 1 15 HELIX 4 4 ALA A 100 GLY A 113 1 14 HELIX 5 5 GLY A 118 ASP A 120 5 3 HELIX 6 6 GLY A 127 GLY A 140 1 14 HELIX 7 7 TYR A 152 GLY A 163 1 12 HELIX 8 8 THR A 184 GLY A 188 5 5 HELIX 9 9 THR A 216 GLY A 231 1 16 HELIX 10 10 TYR A 240 MET A 244 5 5 HELIX 11 11 SER A 251 ILE A 255 5 5 HELIX 12 12 GLY A 257 GLU A 260 5 4 HELIX 13 13 PHE A 268 GLY A 273 1 6 HELIX 14 14 PRO A 295 PHE A 308 1 14 HELIX 15 15 SER A 312 LEU A 323 1 12 HELIX 16 16 THR A 324 LEU A 352 1 29 HELIX 17 17 SER A 373 HIS A 386 1 14 HELIX 18 18 SER A 393 GLU A 400 5 8 HELIX 19 19 HIS A 410 TYR A 425 1 16 HELIX 20 20 ASN B 27 LEU B 33 1 7 HELIX 21 21 TYR B 37 TYR B 53 1 17 HELIX 22 22 PRO B 71 SER B 86 1 16 HELIX 23 23 ALA B 100 GLY B 113 1 14 HELIX 24 24 GLY B 118 ASP B 120 5 3 HELIX 25 25 GLY B 127 GLY B 140 1 14 HELIX 26 26 TYR B 152 GLY B 163 1 12 HELIX 27 27 THR B 184 GLY B 188 5 5 HELIX 28 28 ASP B 192 VAL B 196 5 5 HELIX 29 29 THR B 216 GLY B 231 1 16 HELIX 30 30 TYR B 240 MET B 244 5 5 HELIX 31 31 SER B 251 ILE B 255 5 5 HELIX 32 32 GLY B 257 GLU B 260 5 4 HELIX 33 33 PRO B 295 PHE B 308 1 14 HELIX 34 34 SER B 312 LEU B 323 1 12 HELIX 35 35 THR B 324 SER B 351 1 28 HELIX 36 36 SER B 373 HIS B 386 1 14 HELIX 37 37 SER B 393 GLU B 400 5 8 HELIX 38 38 HIS B 410 TYR B 425 1 16 SHEET 1 A 2 ILE A 59 SER A 60 0 SHEET 2 A 2 VAL A 387 VAL A 388 1 O VAL A 388 N ILE A 59 SHEET 1 B 7 VAL A 122 SER A 125 0 SHEET 2 B 7 GLY A 280 VAL A 283 -1 O GLY A 280 N SER A 125 SHEET 3 B 7 ALA A 262 SER A 267 -1 N GLU A 264 O VAL A 283 SHEET 4 B 7 ILE A 233 ASP A 237 1 N TYR A 236 O THR A 265 SHEET 5 B 7 ILE A 201 CYS A 205 1 N ILE A 202 O VAL A 235 SHEET 6 B 7 ILE A 145 ASP A 149 1 N ALA A 146 O PHE A 203 SHEET 7 B 7 ILE A 178 ARG A 182 1 O MET A 181 N VAL A 147 SHEET 1 C 2 PHE A 168 ASN A 169 0 SHEET 2 C 2 LYS A 174 TYR A 175 -1 O LYS A 174 N ASN A 169 SHEET 1 D 4 VAL A 356 GLY A 358 0 SHEET 2 D 4 TYR A 364 HIS A 368 -1 O TRP A 366 N TYR A 357 SHEET 3 D 4 PHE A 402 SER A 406 -1 O VAL A 405 N VAL A 365 SHEET 4 D 4 THR A 390 PRO A 391 -1 N THR A 390 O ARG A 404 SHEET 1 E 2 ILE B 59 SER B 60 0 SHEET 2 E 2 VAL B 387 VAL B 388 1 O VAL B 388 N ILE B 59 SHEET 1 F 7 VAL B 122 SER B 125 0 SHEET 2 F 7 GLY B 280 VAL B 283 -1 O GLY B 280 N SER B 125 SHEET 3 F 7 ALA B 262 SER B 267 -1 N GLU B 264 O VAL B 283 SHEET 4 F 7 ILE B 233 ASP B 237 1 N TYR B 236 O THR B 265 SHEET 5 F 7 ILE B 201 CYS B 205 1 N PHE B 204 O VAL B 235 SHEET 6 F 7 ILE B 145 ASP B 149 1 N ALA B 146 O PHE B 203 SHEET 7 F 7 GLU B 179 ARG B 182 1 O MET B 181 N VAL B 147 SHEET 1 G 2 PHE B 168 ASN B 169 0 SHEET 2 G 2 LYS B 174 TYR B 175 -1 O LYS B 174 N ASN B 169 SHEET 1 H 4 VAL B 356 GLY B 358 0 SHEET 2 H 4 TYR B 364 HIS B 368 -1 O TRP B 366 N TYR B 357 SHEET 3 H 4 PHE B 402 SER B 406 -1 O VAL B 405 N VAL B 365 SHEET 4 H 4 THR B 390 PRO B 391 -1 N THR B 390 O ARG B 404 LINK NZ LYS B 270 C4A PLP B 501 1555 1555 1.32 CISPEP 1 ASP A 149 PRO A 150 0 9.89 CISPEP 2 SER A 206 PRO A 207 0 -2.81 CISPEP 3 ASN A 209 PRO A 210 0 16.21 CISPEP 4 ALA B 35 GLY B 36 0 11.00 CISPEP 5 ASP B 149 PRO B 150 0 10.01 CISPEP 6 SER B 206 PRO B 207 0 -8.15 CISPEP 7 ASN B 209 PRO B 210 0 12.47 CISPEP 8 GLU B 400 GLY B 401 0 -20.21 SITE 1 AC1 10 PHE A 39 ILE A 63 GLY A 64 TYR A 152 SITE 2 AC1 10 ASN A 209 ARG A 404 PLP A 500 HOH A 603 SITE 3 AC1 10 TYR B 94 ASN B 309 SITE 1 AC2 14 GLY A 127 ALA A 128 LYS A 129 CYS A 205 SITE 2 AC2 14 ASN A 209 ASP A 237 TYR A 240 SER A 267 SITE 3 AC2 14 SER A 269 LYS A 270 ARG A 278 MLT A 433 SITE 4 AC2 14 TYR B 94 ASN B 309 SITE 1 AC3 13 TYR A 94 ASN A 309 GLY B 127 ALA B 128 SITE 2 AC3 13 LYS B 129 TYR B 152 ASN B 209 ASP B 237 SITE 3 AC3 13 TYR B 240 SER B 267 SER B 269 LYS B 270 SITE 4 AC3 13 ARG B 278 CRYST1 102.587 102.587 172.939 90.00 90.00 120.00 P 32 2 1 12 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.009748 0.005628 0.000000 0.00000 SCALE2 0.000000 0.011256 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005782 0.00000