PDB Short entry for 2YXX HEADER LYASE 27-APR-07 2YXX TITLE CRYSTAL STRUCTURE ANALYSIS OF DIAMINOPIMELATE DECARBOXYLATE (LYSA) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIAMINOPIMELATE DECARBOXYLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: LYSA, DAP DECARBOXYLASE; COMPND 5 EC: 4.1.1.20; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA; SOURCE 3 ORGANISM_TAXID: 243274; SOURCE 4 STRAIN: MSB8; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: ROSETTA834(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-21A KEYWDS TM1517, TIM BETA/ALPHA BARREL FOLD, LYASE, STRUCTURAL GENOMICS, KEYWDS 2 NPPSFA, NATIONAL PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL KEYWDS 3 ANALYSES, RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI EXPDTA X-RAY DIFFRACTION AUTHOR Y.NAKAMURA,Y.BESSHO,B.PADMANABHAN,S.YOKOYAMA,RIKEN STRUCTURAL AUTHOR 2 GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 3 13-JUL-11 2YXX 1 VERSN REVDAT 2 24-FEB-09 2YXX 1 VERSN REVDAT 1 30-OCT-07 2YXX 0 JRNL AUTH Y.NAKAMURA,Y.BESSHO,B.PADMANABHAN,S.YOKOYAMA JRNL TITL CRYSTAL STRUCTURE ANALYSIS OF DIAMINOPIMELATE DECARBOXYLATE JRNL TITL 2 (LYSA) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.96 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 476272.230 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 51251 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 SET) : 0.189 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 5184 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.003 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.81 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 7277 REMARK 3 BIN R VALUE (WORKING SET) : 0.2170 REMARK 3 BIN FREE R VALUE : 0.2560 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 828 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.009 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3091 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 16 REMARK 3 SOLVENT ATOMS : 242 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.44000 REMARK 3 B22 (A**2) : -1.38000 REMARK 3 B33 (A**2) : 4.81000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.17 REMARK 3 ESD FROM SIGMAA (A) : 0.07 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.21 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.11 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.032 REMARK 3 BOND ANGLES (DEGREES) : 2.70 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.97 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.38 REMARK 3 BSOL : 46.97 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2YXX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-AUG-07. REMARK 100 THE RCSB ID CODE IS RCSB027273. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 120 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL26B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97898, 0.90000, 0.97946 REMARK 200 MONOCHROMATOR : SI DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU JUPITER 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 60672 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.610 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.61 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.67 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.6 REMARK 200 DATA REDUNDANCY IN SHELL : 5.10 REMARK 200 R MERGE FOR SHELL (I) : 0.36000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40%(V/V) PEG600, 0.1M ACETATE, 0.2M REMARK 280 MGCL2, PH 4.5, OIL-BATCH, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 43.90900 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 49.13800 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 54.65200 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 43.90900 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 49.13800 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 54.65200 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 43.90900 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 49.13800 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 54.65200 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 43.90900 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 49.13800 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 54.65200 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7840 ANGSTROM**2 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 87.81800 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 98.27600 REMARK 350 BIOMT3 2 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 MSE A 1 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NZ LYS A 46 O4A PLP A 401 2.05 REMARK 500 NH2 ARG A 230 O HOH A 602 2.12 REMARK 500 OD1 ASP A 162 OH TYR A 204 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 CE MSE A 378 CE MSE A 378 3656 2.01 REMARK 500 REMARK 500 REMARK: NULL 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 TYR A 18 CG TYR A 18 CD2 0.078 REMARK 500 LYS A 55 CE LYS A 55 NZ 0.156 REMARK 500 GLU A 136 CG GLU A 136 CD 0.117 REMARK 500 ALA A 253 CA ALA A 253 CB 0.129 REMARK 500 CYS A 314 CB CYS A 314 SG -0.104 REMARK 500 GLU A 338 CB GLU A 338 CG -0.160 REMARK 500 MSE A 378 CG MSE A 378 SE 0.505 REMARK 500 MSE A 378 SE MSE A 378 CE 0.562 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 58 NE - CZ - NH2 ANGL. DEV. = -4.5 DEGREES REMARK 500 MSE A 347 CG - SE - CE ANGL. DEV. = -16.5 DEGREES REMARK 500 VAL A 360 CG1 - CB - CG2 ANGL. DEV. = 12.9 DEGREES REMARK 500 MSE A 378 CB - CG - SE ANGL. DEV. = -27.5 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 ASP A 138 104.36 -36.48 REMARK 500 THR A 141 -51.93 168.68 REMARK 500 SER A 170 -18.30 93.87 REMARK 500 SER A 220 18.32 -145.26 REMARK 500 HIS A 269 -119.56 56.36 REMARK 500 ARG A 372 100.59 -163.21 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PLP A 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: TMA001001517.1 RELATED DB: TARGETDB DBREF 2YXX A 1 386 UNP Q9X1K5 DCDA_THEMA 1 386 SEQRES 1 A 386 MSE ASP ILE LEU ARG LYS VAL ALA GLU ILE HIS GLY THR SEQRES 2 A 386 PRO THR TYR VAL TYR PHE GLU GLU THR LEU ARG LYS ARG SEQRES 3 A 386 SER ARG LEU VAL LYS GLU VAL PHE GLU GLY VAL ASN LEU SEQRES 4 A 386 LEU PRO THR PHE ALA VAL LYS ALA ASN ASN ASN PRO VAL SEQRES 5 A 386 LEU LEU LYS ILE LEU ARG GLU GLU GLY PHE GLY MSE ASP SEQRES 6 A 386 VAL VAL THR LYS GLY GLU LEU LEU ALA ALA LYS LEU ALA SEQRES 7 A 386 GLY VAL PRO SER HIS THR VAL VAL TRP ASN GLY ASN GLY SEQRES 8 A 386 LYS SER ARG ASP GLN MSE GLU HIS PHE LEU ARG GLU ASP SEQRES 9 A 386 VAL ARG ILE VAL ASN VAL ASP SER PHE GLU GLU MSE GLU SEQRES 10 A 386 ILE TRP ARG GLU LEU ASN PRO GLU GLY VAL GLU TYR PHE SEQRES 11 A 386 ILE ARG VAL ASN PRO GLU VAL ASP ALA LYS THR HIS PRO SEQRES 12 A 386 HIS ILE SER THR GLY LEU LYS LYS HIS LYS PHE GLY ILE SEQRES 13 A 386 PRO LEU GLU ASP LEU ASP SER PHE MSE GLU ARG PHE ARG SEQRES 14 A 386 SER MSE ASN ILE ARG GLY LEU HIS VAL HIS ILE GLY SER SEQRES 15 A 386 GLN ILE THR ARG VAL GLU PRO PHE VAL GLU ALA PHE SER SEQRES 16 A 386 LYS VAL VAL ARG ALA SER GLU ARG TYR GLY PHE GLU GLU SEQRES 17 A 386 ILE ASN ILE GLY GLY GLY TRP GLY ILE ASN TYR SER GLY SEQRES 18 A 386 GLU GLU LEU ASP LEU SER SER TYR ARG GLU LYS VAL VAL SEQRES 19 A 386 PRO ASP LEU LYS ARG PHE LYS ARG VAL ILE VAL GLU ILE SEQRES 20 A 386 GLY ARG TYR ILE VAL ALA PRO SER GLY TYR LEU LEU LEU SEQRES 21 A 386 ARG VAL VAL LEU VAL LYS ARG ARG HIS ASN LYS ALA PHE SEQRES 22 A 386 VAL VAL VAL ASP GLY GLY MSE ASN VAL LEU ILE ARG PRO SEQRES 23 A 386 ALA LEU TYR SER ALA TYR HIS ARG ILE PHE VAL LEU GLY SEQRES 24 A 386 LYS GLN GLY LYS GLU MSE ARG ALA ASP VAL VAL GLY PRO SEQRES 25 A 386 LEU CYS GLU SER GLY ASP VAL ILE ALA TYR ASP ARG GLU SEQRES 26 A 386 LEU PRO GLU VAL GLU PRO GLY ASP ILE ILE ALA VAL GLU SEQRES 27 A 386 ASN ALA GLY ALA TYR GLY TYR THR MSE SER ASN ASN TYR SEQRES 28 A 386 ASN SER THR THR ARG PRO ALA GLU VAL LEU VAL ARG GLU SEQRES 29 A 386 ASN GLY ARG ILE SER LEU ILE ARG ARG ARG GLU THR GLU SEQRES 30 A 386 MSE ASP ILE PHE LYS ASP VAL VAL MSE MODRES 2YXX MSE A 64 MET SELENOMETHIONINE MODRES 2YXX MSE A 97 MET SELENOMETHIONINE MODRES 2YXX MSE A 116 MET SELENOMETHIONINE MODRES 2YXX MSE A 165 MET SELENOMETHIONINE MODRES 2YXX MSE A 171 MET SELENOMETHIONINE MODRES 2YXX MSE A 280 MET SELENOMETHIONINE MODRES 2YXX MSE A 305 MET SELENOMETHIONINE MODRES 2YXX MSE A 347 MET SELENOMETHIONINE MODRES 2YXX MSE A 378 MET SELENOMETHIONINE MODRES 2YXX MSE A 386 MET SELENOMETHIONINE HET MSE A 64 8 HET MSE A 97 8 HET MSE A 116 8 HET MSE A 165 8 HET MSE A 171 8 HET MSE A 280 8 HET MSE A 305 8 HET MSE A 347 8 HET MSE A 378 8 HET MSE A 386 8 HET PLP A 401 16 HETNAM MSE SELENOMETHIONINE HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETSYN PLP VITAMIN B6 PHOSPHATE FORMUL 1 MSE 10(C5 H11 N O2 SE) FORMUL 2 PLP C8 H10 N O6 P FORMUL 3 HOH *242(H2 O) HELIX 1 1 ASP A 2 GLY A 12 1 11 HELIX 2 2 GLU A 20 PHE A 34 1 15 HELIX 3 3 LYS A 46 ASN A 48 5 3 HELIX 4 4 ASN A 50 GLU A 60 1 11 HELIX 5 5 THR A 68 ALA A 78 1 11 HELIX 6 6 PRO A 81 HIS A 83 5 3 HELIX 7 7 SER A 93 GLU A 103 1 11 HELIX 8 8 SER A 112 ASN A 123 1 12 HELIX 9 9 HIS A 142 HIS A 152 1 11 HELIX 10 10 ASP A 160 ARG A 169 1 10 HELIX 11 11 VAL A 187 GLY A 205 1 19 HELIX 12 12 ASP A 225 VAL A 233 1 9 HELIX 13 13 VAL A 234 LYS A 238 5 5 HELIX 14 14 GLY A 248 ALA A 253 1 6 HELIX 15 15 ILE A 284 TYR A 289 1 6 HELIX 16 16 GLY A 344 SER A 348 5 5 HELIX 17 17 THR A 376 PHE A 381 1 6 SHEET 1 A 6 ILE A 295 VAL A 297 0 SHEET 2 A 6 ILE A 334 VAL A 337 -1 O ALA A 336 N PHE A 296 SHEET 3 A 6 GLY A 256 ARG A 268 -1 N LEU A 260 O ILE A 335 SHEET 4 A 6 LYS A 271 VAL A 276 -1 O VAL A 275 N VAL A 263 SHEET 5 A 6 MSE A 305 VAL A 310 1 O ASP A 308 N VAL A 274 SHEET 6 A 6 VAL A 319 LEU A 326 -1 O ALA A 321 N VAL A 309 SHEET 1 B 6 ILE A 295 VAL A 297 0 SHEET 2 B 6 ILE A 334 VAL A 337 -1 O ALA A 336 N PHE A 296 SHEET 3 B 6 GLY A 256 ARG A 268 -1 N LEU A 260 O ILE A 335 SHEET 4 B 6 THR A 15 PHE A 19 -1 N THR A 15 O LEU A 259 SHEET 5 B 6 ALA A 358 VAL A 362 1 O VAL A 362 N TYR A 18 SHEET 6 B 6 ILE A 368 ARG A 372 -1 O SER A 369 N LEU A 361 SHEET 1 C10 ILE A 156 PRO A 157 0 SHEET 2 C10 GLU A 128 ASN A 134 1 N ARG A 132 O ILE A 156 SHEET 3 C10 ILE A 173 HIS A 177 1 O ARG A 174 N TYR A 129 SHEET 4 C10 GLU A 208 ASN A 210 1 O ASN A 210 N LEU A 176 SHEET 5 C10 ARG A 242 ILE A 247 1 O ILE A 244 N ILE A 209 SHEET 6 C10 LEU A 39 ALA A 44 1 N LEU A 40 O VAL A 243 SHEET 7 C10 GLY A 63 VAL A 66 1 O ASP A 65 N PHE A 43 SHEET 8 C10 VAL A 85 TRP A 87 1 O VAL A 86 N MSE A 64 SHEET 9 C10 ILE A 107 VAL A 110 1 O ASN A 109 N TRP A 87 SHEET 10 C10 GLU A 128 ASN A 134 1 O PHE A 130 N VAL A 108 LINK C GLY A 63 N MSE A 64 1555 1555 1.30 LINK C MSE A 64 N ASP A 65 1555 1555 1.33 LINK C GLN A 96 N MSE A 97 1555 1555 1.35 LINK C MSE A 97 N GLU A 98 1555 1555 1.35 LINK C GLU A 115 N MSE A 116 1555 1555 1.33 LINK C MSE A 116 N GLU A 117 1555 1555 1.34 LINK C PHE A 164 N MSE A 165 1555 1555 1.32 LINK C MSE A 165 N GLU A 166 1555 1555 1.32 LINK C SER A 170 N MSE A 171 1555 1555 1.32 LINK C MSE A 171 N ASN A 172 1555 1555 1.36 LINK C GLY A 279 N MSE A 280 1555 1555 1.32 LINK C MSE A 280 N ASN A 281 1555 1555 1.35 LINK C GLU A 304 N MSE A 305 1555 1555 1.34 LINK C MSE A 305 N ARG A 306 1555 1555 1.34 LINK C THR A 346 N MSE A 347 1555 1555 1.31 LINK C MSE A 347 N SER A 348 1555 1555 1.34 LINK C GLU A 377 N MSE A 378 1555 1555 1.33 LINK C MSE A 378 N ASP A 379 1555 1555 1.33 LINK C VAL A 385 N MSE A 386 1555 1555 1.32 CISPEP 1 THR A 13 PRO A 14 0 -1.27 SITE 1 AC1 13 LYS A 46 ASP A 65 HIS A 179 SER A 182 SITE 2 AC1 13 GLY A 214 GLU A 246 GLY A 248 ARG A 249 SITE 3 AC1 13 CYS A 314 TYR A 343 HOH A 404 HOH A 450 SITE 4 AC1 13 HOH A 612 CRYST1 87.818 98.276 109.304 90.00 90.00 90.00 I 2 2 2 8 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 0.011387 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010175 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009149 0.00000