PDB Short entry for 3R5F HEADER LIGASE 18-MAR-11 3R5F TITLE CRYSTAL STRUCTURE OF D-ALANINE-D-ALNINE LIGASE FROM XANTHOMONAS ORYZAE TITLE 2 PV. ORYZAE WITH ATP COMPND MOL_ID: 1; COMPND 2 MOLECULE: D-ALANINE--D-ALANINE LIGASE 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: D-ALA-D-ALA LIGASE 1, D-ALANYLALANINE SYNTHETASE 1; COMPND 5 EC: 6.3.2.4; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: XANTHOMONAS ORYZAE PV. ORYZAE; SOURCE 3 ORGANISM_TAXID: 291331; SOURCE 4 STRAIN: KACC10331; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: HIS-TEV-PET11A KEYWDS XODDL-ATP COMPLEX, ATP-GRASP DOMAIN, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR T.T.N.DOAN,J.K.KIM,L.W.KANG REVDAT 2 01-NOV-23 3R5F 1 REMARK SEQADV LINK REVDAT 1 25-MAY-11 3R5F 0 JRNL AUTH T.T.N.DOAN,J.K.KIM,L.W.KANG JRNL TITL CRYSTAL STRUCTURE OF D-ALANINE-D-ALANINE LIGASE A FROM JRNL TITL 2 XANTHOMONAS ORYZAE PATHOVAR ORYZAE WITH ATP JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.07 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 2.07 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.95 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 20294 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) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.277 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1097 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) : 2.07 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.12 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1471 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2300 REMARK 3 BIN FREE R VALUE SET COUNT : 77 REMARK 3 BIN FREE R VALUE : 0.3330 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2586 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 125 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.19 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01000 REMARK 3 B22 (A**2) : -0.01000 REMARK 3 B33 (A**2) : 0.01000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.216 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.152 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.454 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.915 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2676 ; 0.023 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3643 ; 2.098 ; 1.978 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 342 ; 7.522 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 117 ;38.771 ;23.932 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 430 ;19.745 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;25.896 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 429 ; 0.147 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2010 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1710 ; 1.281 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2733 ; 2.228 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 966 ; 3.276 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 910 ; 5.277 ; 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 : 1.40 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 3R5F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-MAR-11. REMARK 100 THE DEPOSITION ID IS D_1000064511. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-DEC-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21461 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.070 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL 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) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 3E5N REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.001ML OF 6 MG/ML PROTEIN WAS MIXED REMARK 280 TO 0.001ML OF A MOTHER LIQUOR, CONTAINING 30%(W/V) PEG 4000, REMARK 280 0.1M TRIS PH 8.0, 0.2M MGCL2, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 283K, PH 8.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 48.57150 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 41.61250 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 41.61250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 72.85725 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 41.61250 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 41.61250 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 24.28575 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 41.61250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 41.61250 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 72.85725 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 41.61250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 41.61250 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 24.28575 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 48.57150 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 REMARK 350 TOTAL BURIED SURFACE AREA: 4490 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.0 KCAL/MOL 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 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 48.57150 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 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLU A -7 REMARK 465 ASN A -6 REMARK 465 LEU A -5 REMARK 465 TYR A -4 REMARK 465 PHE A -3 REMARK 465 GLN A -2 REMARK 465 GLY A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 ARG A 2 REMARK 465 PRO A 92 REMARK 465 GLU A 93 REMARK 465 GLN A 94 REMARK 465 HIS A 250 REMARK 465 ASP A 251 REMARK 465 ALA A 252 REMARK 465 PHE A 253 REMARK 465 TYR A 254 REMARK 465 SER A 255 REMARK 465 TYR A 256 REMARK 465 ALA A 257 REMARK 465 THR A 258 REMARK 465 LYS A 259 REMARK 465 TYR A 260 REMARK 465 ILE A 261 REMARK 465 SER A 262 REMARK 465 GLU A 263 REMARK 465 HIS A 264 REMARK 465 GLY A 265 REMARK 465 ALA A 266 REMARK 465 LEU A 366 REMARK 465 HIS A 367 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 ALA A 307 N - CA - C ANGL. DEV. = -16.3 DEGREES REMARK 500 ASP A 308 N - CA - C ANGL. DEV. = 18.6 DEGREES REMARK 500 GLY A 309 C - N - CA ANGL. DEV. = 14.9 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 ASN A 236 -97.34 -98.43 REMARK 500 ASP A 308 10.90 96.03 REMARK 500 VAL A 364 156.42 138.32 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 ASP A 308 GLY A 309 -74.75 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 369 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 302 OD2 REMARK 620 2 ATP A 368 O1A 174.9 REMARK 620 3 ATP A 368 O3G 120.3 56.2 REMARK 620 4 HOH A 480 O 61.3 113.7 72.4 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ATP A 368 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 369 DBREF 3R5F A 1 367 UNP Q2P8P8 Q2P8P8_XANOM 1 367 SEQADV 3R5F HIS A -16 UNP Q2P8P8 EXPRESSION TAG SEQADV 3R5F HIS A -15 UNP Q2P8P8 EXPRESSION TAG SEQADV 3R5F HIS A -14 UNP Q2P8P8 EXPRESSION TAG SEQADV 3R5F HIS A -13 UNP Q2P8P8 EXPRESSION TAG SEQADV 3R5F HIS A -12 UNP Q2P8P8 EXPRESSION TAG SEQADV 3R5F HIS A -11 UNP Q2P8P8 EXPRESSION TAG SEQADV 3R5F HIS A -10 UNP Q2P8P8 EXPRESSION TAG SEQADV 3R5F SER A -9 UNP Q2P8P8 EXPRESSION TAG SEQADV 3R5F SER A -8 UNP Q2P8P8 EXPRESSION TAG SEQADV 3R5F GLU A -7 UNP Q2P8P8 EXPRESSION TAG SEQADV 3R5F ASN A -6 UNP Q2P8P8 EXPRESSION TAG SEQADV 3R5F LEU A -5 UNP Q2P8P8 EXPRESSION TAG SEQADV 3R5F TYR A -4 UNP Q2P8P8 EXPRESSION TAG SEQADV 3R5F PHE A -3 UNP Q2P8P8 EXPRESSION TAG SEQADV 3R5F GLN A -2 UNP Q2P8P8 EXPRESSION TAG SEQADV 3R5F GLY A -1 UNP Q2P8P8 EXPRESSION TAG SEQADV 3R5F HIS A 0 UNP Q2P8P8 EXPRESSION TAG SEQADV 3R5F VAL A 327 UNP Q2P8P8 MET 327 ENGINEERED MUTATION SEQRES 1 A 384 HIS HIS HIS HIS HIS HIS HIS SER SER GLU ASN LEU TYR SEQRES 2 A 384 PHE GLN GLY HIS MET ARG LYS ILE ARG VAL GLY LEU ILE SEQRES 3 A 384 PHE GLY GLY LYS SER ALA GLU HIS GLU VAL SER LEU GLN SEQRES 4 A 384 SER ALA ARG ASN ILE LEU ASP ALA LEU ASP PRO GLN ARG SEQRES 5 A 384 PHE GLU PRO VAL LEU ILE GLY ILE ASP LYS GLN GLY GLN SEQRES 6 A 384 TRP HIS VAL ASN ASP PRO ASP SER PHE LEU LEU HIS ALA SEQRES 7 A 384 ASP ASP PRO ALA ARG ILE ALA LEU HIS ARG SER GLY ARG SEQRES 8 A 384 GLY VAL ALA LEU LEU PRO GLY ALA GLN GLN GLN GLN LEU SEQRES 9 A 384 ARG PRO ILE GLN PRO GLU GLN ALA LEU ALA GLN ILE ASP SEQRES 10 A 384 VAL VAL PHE PRO ILE VAL HIS GLY THR LEU GLY GLU ASP SEQRES 11 A 384 GLY SER LEU GLN GLY LEU LEU ARG MET ALA ASN LEU PRO SEQRES 12 A 384 PHE VAL GLY SER GLY VAL LEU GLY SER ALA VAL ALA MET SEQRES 13 A 384 ASP LYS ASP MET ALA LYS ARG VAL LEU ARG ASP ALA ARG SEQRES 14 A 384 LEU ALA VAL ALA PRO PHE VAL CYS PHE ASP ARG HIS THR SEQRES 15 A 384 ALA ALA HIS ALA ASP VAL ASP THR LEU ILE ALA GLN LEU SEQRES 16 A 384 GLY LEU PRO LEU PHE VAL LYS PRO ALA ASN GLN GLY SER SEQRES 17 A 384 SER VAL GLY VAL SER GLN VAL ARG THR ALA ASP ALA PHE SEQRES 18 A 384 ALA ALA ALA LEU ALA LEU ALA LEU ALA TYR ASP HIS LYS SEQRES 19 A 384 VAL LEU VAL GLU ALA ALA VAL ALA GLY ARG GLU ILE GLU SEQRES 20 A 384 CYS ALA VAL LEU GLY ASN ALA VAL PRO HIS ALA SER VAL SEQRES 21 A 384 CYS GLY GLU VAL VAL VAL HIS ASP ALA PHE TYR SER TYR SEQRES 22 A 384 ALA THR LYS TYR ILE SER GLU HIS GLY ALA GLU ILE VAL SEQRES 23 A 384 ILE PRO ALA ASP ILE ASP ALA GLN THR GLN GLN ARG ILE SEQRES 24 A 384 GLN GLN ILE ALA VAL GLN ALA TYR GLN ALA LEU GLY CYS SEQRES 25 A 384 ALA GLY MET ALA ARG VAL ASP VAL PHE LEU CYS ALA ASP SEQRES 26 A 384 GLY ARG ILE VAL ILE ASN GLU VAL ASN THR LEU PRO GLY SEQRES 27 A 384 PHE THR ARG ILE SER VAL TYR PRO LYS LEU TRP GLN ALA SEQRES 28 A 384 SER GLY LEU ASP TYR ARG GLY LEU ILE THR ARG LEU ILE SEQRES 29 A 384 GLU LEU ALA LEU GLU ARG HIS THR ASP ASP GLN LEU LEU SEQRES 30 A 384 ARG SER ALA VAL GLU LEU HIS HET ATP A 368 31 HET MG A 369 1 HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 2 ATP C10 H16 N5 O13 P3 FORMUL 3 MG MG 2+ FORMUL 4 HOH *125(H2 O) HELIX 1 1 GLU A 16 LEU A 31 1 16 HELIX 2 2 GLY A 108 ASP A 113 1 6 HELIX 3 3 GLY A 114 ALA A 123 1 10 HELIX 4 4 GLY A 131 ASP A 140 1 10 HELIX 5 5 ASP A 140 ALA A 151 1 12 HELIX 6 6 ARG A 163 ALA A 167 1 5 HELIX 7 7 ASP A 170 GLY A 179 1 10 HELIX 8 8 THR A 200 ASP A 202 5 3 HELIX 9 9 ALA A 203 LEU A 212 1 10 HELIX 10 10 ASP A 275 GLY A 294 1 20 HELIX 11 11 SER A 326 ALA A 334 1 9 HELIX 12 12 ASP A 338 ALA A 363 1 26 SHEET 1 A 4 TRP A 49 ASN A 52 0 SHEET 2 A 4 PHE A 36 ILE A 43 -1 N GLY A 42 O HIS A 50 SHEET 3 A 4 ILE A 4 GLY A 11 1 N VAL A 6 O GLU A 37 SHEET 4 A 4 VAL A 101 VAL A 106 1 O VAL A 101 N GLY A 7 SHEET 1 B 2 LEU A 58 LEU A 59 0 SHEET 2 B 2 ALA A 68 LEU A 69 -1 O ALA A 68 N LEU A 59 SHEET 1 C 2 VAL A 76 LEU A 78 0 SHEET 2 C 2 LEU A 87 PRO A 89 -1 O ARG A 88 N ALA A 77 SHEET 1 D 6 ALA A 154 VAL A 155 0 SHEET 2 D 6 ILE A 311 ASN A 317 1 O ILE A 313 N ALA A 154 SHEET 3 D 6 MET A 298 LEU A 305 -1 N ARG A 300 O ASN A 317 SHEET 4 D 6 ARG A 227 LEU A 234 -1 N CYS A 231 O VAL A 301 SHEET 5 D 6 HIS A 240 VAL A 247 -1 O HIS A 240 N LEU A 234 SHEET 6 D 6 ILE A 268 VAL A 269 -1 O VAL A 269 N GLU A 246 SHEET 1 E 4 PHE A 158 ASP A 162 0 SHEET 2 E 4 LYS A 217 ALA A 222 -1 O VAL A 218 N PHE A 161 SHEET 3 E 4 LEU A 182 PRO A 186 -1 N LYS A 185 O LEU A 219 SHEET 4 E 4 SER A 196 VAL A 198 -1 O VAL A 198 N LEU A 182 LINK OD2 ASP A 302 MG MG A 369 1555 1555 2.63 LINK O1A ATP A 368 MG MG A 369 1555 1555 2.77 LINK O3G ATP A 368 MG MG A 369 1555 1555 2.88 LINK MG MG A 369 O HOH A 480 1555 1555 2.62 CISPEP 1 LEU A 180 PRO A 181 0 -2.42 CISPEP 2 ILE A 270 PRO A 271 0 -8.31 SITE 1 AC1 16 LYS A 141 PHE A 183 LYS A 185 SER A 191 SITE 2 AC1 16 SER A 192 GLU A 221 ALA A 222 ALA A 223 SITE 3 AC1 16 VAL A 224 GLU A 228 PHE A 304 ASN A 314 SITE 4 AC1 16 GLU A 315 MG A 369 HOH A 476 HOH A 479 SITE 1 AC2 5 ASP A 302 ASN A 314 GLU A 315 ATP A 368 SITE 2 AC2 5 HOH A 480 CRYST1 83.225 83.225 97.143 90.00 90.00 90.00 P 43 21 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 0.012016 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012016 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010294 0.00000