HEADER HYDROLASE 16-MAY-07 2PYU TITLE STRUCTURE OF THE E. COLI INOSINE TRIPHOSPHATE PYROPHOSPHATASE RGDB IN TITLE 2 COMPLEX WITH IMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: INOSINE TRIPHOSPHATE PYROPHOSPHATASE RDGB; COMPND 3 CHAIN: A; COMPND 4 EC: 3.6.1.19; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: YGGV; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) CODON PLUS RP; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15-B-BASED,P11 KEYWDS ITP PYROPHOSPHATASE X-RAY STRUCTURE ENZYME MECHANISM PRODUCT, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.U.SINGER,M.PROUDFOOT,T.SKARINA,A.SAVCHENKO,A.F.YAKUNIN REVDAT 5 30-AUG-23 2PYU 1 REMARK REVDAT 4 20-OCT-21 2PYU 1 REMARK SEQADV REVDAT 3 13-JUL-11 2PYU 1 VERSN REVDAT 2 24-FEB-09 2PYU 1 VERSN REVDAT 1 18-MAR-08 2PYU 0 JRNL AUTH A.SAVCHENKO,M.PROUDFOOT,T.SKARINA,A.SINGER,O.LITVINOVA, JRNL AUTH 2 R.SANISHVILI,G.BROWN,N.CHIRGADZE,A.F.YAKUNIN JRNL TITL MOLECULAR BASIS OF THE ANTIMUTAGENIC ACTIVITY OF THE JRNL TITL 2 HOUSE-CLEANING INOSINE TRIPHOSPHATE PYROPHOSPHATASE RDGB JRNL TITL 3 FROM ESCHERICHIA COLI. JRNL REF J.MOL.BIOL. V. 374 1091 2007 JRNL REFN ISSN 0022-2836 JRNL PMID 17976651 JRNL DOI 10.1016/J.JMB.2007.10.012 REMARK 2 REMARK 2 RESOLUTION. 2.02 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) : 2.02 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.03 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 16119 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) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 860 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) : 2.02 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.07 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1160 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.51 REMARK 3 BIN R VALUE (WORKING SET) : 0.2470 REMARK 3 BIN FREE R VALUE SET COUNT : 65 REMARK 3 BIN FREE R VALUE : 0.3200 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1559 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 27 REMARK 3 SOLVENT ATOMS : 147 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.28 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.02000 REMARK 3 B22 (A**2) : 0.02000 REMARK 3 B33 (A**2) : -0.05000 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): 0.172 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.171 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.117 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.241 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.923 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1628 ; 0.026 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2212 ; 2.236 ; 1.986 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 209 ; 7.032 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 67 ;34.935 ;23.731 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 261 ;14.233 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;21.644 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 253 ; 0.163 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1224 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 752 ; 0.229 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1113 ; 0.312 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 117 ; 0.157 ; 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): 57 ; 0.229 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 9 ; 0.112 ; 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): 1067 ; 1.517 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1653 ; 2.298 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 634 ; 3.814 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 559 ; 5.629 ; 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 : BABINET MODEL WITH 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: NULL REMARK 4 REMARK 4 2PYU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-MAY-07. REMARK 100 THE DEPOSITION ID IS D_1000042935. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-MAR-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : OSMIC MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31488 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.020 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 37.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.02 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.09 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 0.47600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB CODE 1K7K REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG3350, 200 MM MG ACETATE, REMARK 280 CRYOPROTECTED WITH 7% EACH OF GLYCEROL, SUCROSE AND ETHYLENE REMARK 280 GLYCOL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 40.53650 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 38.97050 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 38.97050 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 60.80475 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 38.97050 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 38.97050 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 20.26825 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 38.97050 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 38.97050 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 60.80475 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 38.97050 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 38.97050 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 20.26825 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 40.53650 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 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 40.53650 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 -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 GLY A 197 REMARK 465 GLY A 198 REMARK 465 SER A 199 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASN A 196 CG OD1 ND2 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 VAL A 123 CB VAL A 123 CG2 -0.142 REMARK 500 CYS A 136 CB CYS A 136 SG 0.113 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 LEU A 191 CA - CB - CG ANGL. DEV. = 15.7 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 HIS A -10 140.06 143.50 REMARK 500 HIS A -10 140.65 155.74 REMARK 500 ARG A -3 77.49 -118.70 REMARK 500 THR A 145 -177.71 -69.56 REMARK 500 LEU A 194 35.05 -95.08 REMARK 500 ARG A 195 16.44 -147.70 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 HIS A -11 HIS A -10 148.64 REMARK 500 REMARK 500 REMARK: NULL REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 IMP A 3036 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IMP A 3036 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 600 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1K7K RELATED DB: PDB REMARK 900 STRUCTURE OF APO-RGDB REMARK 900 RELATED ID: 2Q16 RELATED DB: PDB REMARK 900 YGGV PLUS ITP DBREF 2PYU A 1 197 UNP P52061 HAM1_ECOLI 1 197 SEQADV 2PYU MET A -19 UNP P52061 EXPRESSION TAG SEQADV 2PYU GLY A -18 UNP P52061 EXPRESSION TAG SEQADV 2PYU SER A -17 UNP P52061 EXPRESSION TAG SEQADV 2PYU SER A -16 UNP P52061 EXPRESSION TAG SEQADV 2PYU HIS A -15 UNP P52061 EXPRESSION TAG SEQADV 2PYU HIS A -14 UNP P52061 EXPRESSION TAG SEQADV 2PYU HIS A -13 UNP P52061 EXPRESSION TAG SEQADV 2PYU HIS A -12 UNP P52061 EXPRESSION TAG SEQADV 2PYU HIS A -11 UNP P52061 EXPRESSION TAG SEQADV 2PYU HIS A -10 UNP P52061 EXPRESSION TAG SEQADV 2PYU SER A -9 UNP P52061 EXPRESSION TAG SEQADV 2PYU SER A -8 UNP P52061 EXPRESSION TAG SEQADV 2PYU GLY A -7 UNP P52061 EXPRESSION TAG SEQADV 2PYU LEU A -6 UNP P52061 EXPRESSION TAG SEQADV 2PYU VAL A -5 UNP P52061 EXPRESSION TAG SEQADV 2PYU PRO A -4 UNP P52061 EXPRESSION TAG SEQADV 2PYU ARG A -3 UNP P52061 EXPRESSION TAG SEQADV 2PYU GLY A -2 UNP P52061 EXPRESSION TAG SEQADV 2PYU SER A -1 UNP P52061 EXPRESSION TAG SEQADV 2PYU HIS A 0 UNP P52061 EXPRESSION TAG SEQADV 2PYU ALA A 69 UNP P52061 ASP 69 ENGINEERED MUTATION SEQADV 2PYU GLY A 198 UNP P52061 EXPRESSION TAG SEQADV 2PYU SER A 199 UNP P52061 EXPRESSION TAG SEQRES 1 A 219 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 219 LEU VAL PRO ARG GLY SER HIS MET GLN LYS VAL VAL LEU SEQRES 3 A 219 ALA THR GLY ASN VAL GLY LYS VAL ARG GLU LEU ALA SER SEQRES 4 A 219 LEU LEU SER ASP PHE GLY LEU ASP ILE VAL ALA GLN THR SEQRES 5 A 219 ASP LEU GLY VAL ASP SER ALA GLU GLU THR GLY LEU THR SEQRES 6 A 219 PHE ILE GLU ASN ALA ILE LEU LYS ALA ARG HIS ALA ALA SEQRES 7 A 219 LYS VAL THR ALA LEU PRO ALA ILE ALA ASP ALA SER GLY SEQRES 8 A 219 LEU ALA VAL ASP VAL LEU GLY GLY ALA PRO GLY ILE TYR SEQRES 9 A 219 SER ALA ARG TYR SER GLY GLU ASP ALA THR ASP GLN LYS SEQRES 10 A 219 ASN LEU GLN LYS LEU LEU GLU THR MET LYS ASP VAL PRO SEQRES 11 A 219 ASP ASP GLN ARG GLN ALA ARG PHE HIS CYS VAL LEU VAL SEQRES 12 A 219 TYR LEU ARG HIS ALA GLU ASP PRO THR PRO LEU VAL CYS SEQRES 13 A 219 HIS GLY SER TRP PRO GLY VAL ILE THR ARG GLU PRO ALA SEQRES 14 A 219 GLY THR GLY GLY PHE GLY TYR ASP PRO ILE PHE PHE VAL SEQRES 15 A 219 PRO SER GLU GLY LYS THR ALA ALA GLU LEU THR ARG GLU SEQRES 16 A 219 GLU LYS SER ALA ILE SER HIS ARG GLY GLN ALA LEU LYS SEQRES 17 A 219 LEU LEU LEU ASP ALA LEU ARG ASN GLY GLY SER HET IMP A3036 46 HET EDO A 600 4 HETNAM IMP INOSINIC ACID HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 IMP C10 H13 N4 O8 P FORMUL 3 EDO C2 H6 O2 FORMUL 4 HOH *147(H2 O) HELIX 1 1 ASN A 10 SER A 22 1 13 HELIX 2 2 THR A 45 ALA A 62 1 18 HELIX 3 3 VAL A 76 GLY A 78 5 3 HELIX 4 4 PRO A 81 TYR A 88 5 8 HELIX 5 5 THR A 94 LYS A 107 1 14 HELIX 6 6 PRO A 110 GLN A 113 5 4 HELIX 7 7 TYR A 156 PRO A 158 5 3 HELIX 8 8 VAL A 162 GLY A 166 5 5 HELIX 9 9 THR A 168 LEU A 172 5 5 HELIX 10 10 THR A 173 SER A 181 1 9 HELIX 11 11 SER A 181 LEU A 194 1 14 SHEET 1 A 6 LEU A 26 ALA A 30 0 SHEET 2 A 6 GLN A 2 LEU A 6 1 N GLN A 2 O ASP A 27 SHEET 3 A 6 ALA A 65 VAL A 74 1 O ILE A 66 N VAL A 5 SHEET 4 A 6 GLN A 115 LEU A 125 -1 O VAL A 121 N ALA A 69 SHEET 5 A 6 LEU A 134 ILE A 144 -1 O CYS A 136 N LEU A 122 SHEET 6 A 6 PHE A 160 PHE A 161 -1 O PHE A 161 N VAL A 143 CISPEP 1 ARG A -3 GLY A -2 0 -13.60 CISPEP 2 ALA A 80 PRO A 81 0 -4.62 CISPEP 3 ARG A 195 ASN A 196 0 -18.29 SITE 1 AC1 13 SER A 70 GLY A 71 SER A 85 ALA A 86 SITE 2 AC1 13 PHE A 118 PHE A 154 TYR A 156 ASP A 157 SITE 3 AC1 13 LYS A 177 HIS A 182 HOH A3067 HOH A3074 SITE 4 AC1 13 HOH A3106 SITE 1 AC2 4 PRO A 81 GLY A 82 ILE A 83 HOH A3040 CRYST1 77.941 77.941 81.073 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 0.012830 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012830 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012335 0.00000