HEADER ISOMERASE 04-JUN-15 5BUV TITLE X-RAY STRUCTURE OF WBCA FROM YERSINIA ENTEROCOLITICA COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE EPIMERASE; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: WBCA; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: YERSINIA ENTEROCOLITICA SUBSP. ENTEROCOLITICA SOURCE 3 8081; SOURCE 4 ORGANISM_TAXID: 393305; SOURCE 5 STRAIN: NCTC 13174 / 8081; SOURCE 6 GENE: WBCA, YE3085; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: ROSETTA2(DE3) KEYWDS LIPOPOLYSACCHARIDE, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR H.M.HOLDEN,A.J.SALINGER,H.A.BROWN,J.B.THODEN REVDAT 5 27-SEP-23 5BUV 1 REMARK REVDAT 4 15-NOV-17 5BUV 1 SOURCE JRNL REMARK REVDAT 3 28-OCT-15 5BUV 1 JRNL REVDAT 2 26-AUG-15 5BUV 1 JRNL REVDAT 1 05-AUG-15 5BUV 0 JRNL AUTH A.J.SALINGER,H.A.BROWN,J.B.THODEN,H.M.HOLDEN JRNL TITL BIOCHEMICAL STUDIES ON WBCA, A SUGAR EPIMERASE FROM YERSINIA JRNL TITL 2 ENTEROCOLITICA. JRNL REF PROTEIN SCI. V. 24 1633 2015 JRNL REFN ESSN 1469-896X JRNL PMID 26174084 JRNL DOI 10.1002/PRO.2747 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.36 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 47639 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 : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2541 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) : 1.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.80 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3422 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.30 REMARK 3 BIN R VALUE (WORKING SET) : 0.2980 REMARK 3 BIN FREE R VALUE SET COUNT : 191 REMARK 3 BIN FREE R VALUE : 0.3280 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4253 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 45 REMARK 3 SOLVENT ATOMS : 400 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.78 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.03000 REMARK 3 B33 (A**2) : -0.03000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.03000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.140 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.140 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.107 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.442 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.918 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4449 ; 0.011 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4073 ; 0.000 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6024 ; 1.998 ; 1.941 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9399 ; 0.808 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 536 ; 7.182 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 231 ;31.484 ;24.156 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 754 ;14.599 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;14.343 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 627 ; 0.121 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5076 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1122 ; 0.001 ; 0.020 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 5BUV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-JUN-15. REMARK 100 THE DEPOSITION ID IS D_1000210575. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-NOV-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : NULL 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 RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER PLATINUM 135 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SAINT REMARK 200 DATA SCALING SOFTWARE : SADABS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 50180 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08200 REMARK 200 FOR THE DATA SET : 6.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.50 REMARK 200 R MERGE FOR SHELL (I) : 0.34100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 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: 4HN0 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 14-18% PEG5000-OME, 5 MM CPD-6 REMARK 280 -DEOXYGULOSE, 2% GLYCEROL, 100 MM MOPS, PH 7, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z 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 39.58000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.33900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 39.58000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 21.33900 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4600 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4680 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14990 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -37.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 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 GLY A -3 REMARK 465 HIS A -2 REMARK 465 MET A -1 REMARK 465 PHE A 174 REMARK 465 GLY B -3 REMARK 465 HIS B -2 REMARK 465 MET B -1 REMARK 465 ALA B 0 REMARK 465 PHE B 174 REMARK 465 GLY C -3 REMARK 465 PHE C 174 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 HIS C -2 CG ND1 CD2 CE1 NE2 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 O HOH C 421 O HOH C 435 2.05 REMARK 500 O HOH C 418 O HOH C 436 2.06 REMARK 500 ND2 ASN A 169 O HOH A 301 2.07 REMARK 500 OE2 GLU A 7 O HOH A 302 2.08 REMARK 500 O HOH A 441 O HOH C 361 2.13 REMARK 500 O3 PO4 A 202 O HOH A 303 2.14 REMARK 500 O1 PO4 B 202 O HOH B 301 2.16 REMARK 500 O HOH A 373 O HOH A 443 2.16 REMARK 500 O HOH C 405 O HOH C 422 2.17 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 MET A 125 CG - SD - CE ANGL. DEV. = -14.7 DEGREES REMARK 500 ASP A 127 CB - CG - OD1 ANGL. DEV. = 6.9 DEGREES REMARK 500 ASP B 70 CB - CG - OD2 ANGL. DEV. = 5.7 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 SER A 46 30.94 -144.67 REMARK 500 SER B 46 20.00 -142.54 REMARK 500 GLU B 81 141.09 -174.06 REMARK 500 SER C 46 29.56 -141.64 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 392 DISTANCE = 5.98 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CYT A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CYT B 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 C 201 DBREF 5BUV A 2 174 UNP A1JNA0 A1JNA0_YERE8 2 174 DBREF 5BUV B 2 174 UNP A1JNA0 A1JNA0_YERE8 2 174 DBREF 5BUV C 2 174 UNP A1JNA0 A1JNA0_YERE8 2 174 SEQADV 5BUV GLY A -3 UNP A1JNA0 EXPRESSION TAG SEQADV 5BUV HIS A -2 UNP A1JNA0 EXPRESSION TAG SEQADV 5BUV MET A -1 UNP A1JNA0 EXPRESSION TAG SEQADV 5BUV ALA A 0 UNP A1JNA0 EXPRESSION TAG SEQADV 5BUV SER A 1 UNP A1JNA0 EXPRESSION TAG SEQADV 5BUV GLY B -3 UNP A1JNA0 EXPRESSION TAG SEQADV 5BUV HIS B -2 UNP A1JNA0 EXPRESSION TAG SEQADV 5BUV MET B -1 UNP A1JNA0 EXPRESSION TAG SEQADV 5BUV ALA B 0 UNP A1JNA0 EXPRESSION TAG SEQADV 5BUV SER B 1 UNP A1JNA0 EXPRESSION TAG SEQADV 5BUV GLY C -3 UNP A1JNA0 EXPRESSION TAG SEQADV 5BUV HIS C -2 UNP A1JNA0 EXPRESSION TAG SEQADV 5BUV MET C -1 UNP A1JNA0 EXPRESSION TAG SEQADV 5BUV ALA C 0 UNP A1JNA0 EXPRESSION TAG SEQADV 5BUV SER C 1 UNP A1JNA0 EXPRESSION TAG SEQRES 1 A 178 GLY HIS MET ALA SER ILE ILE ASN ILE THR GLU LEU ASN SEQRES 2 A 178 ILE SER GLY CYS TYR LEU ILE GLU SER PRO ILE PHE SER SEQRES 3 A 178 ASP GLU ARG GLY GLU PHE VAL LYS THR HIS HIS GLN GLU SEQRES 4 A 178 ILE PHE LYS ASN PHE GLY LEU GLU ILE PRO SER ALA GLU SEQRES 5 A 178 GLU TYR TYR SER ARG SER LYS ASN ASN VAL ILE ARG GLY SEQRES 6 A 178 MET HIS PHE GLN GLN TYR PRO ASP ASP HIS ASN LYS LEU SEQRES 7 A 178 VAL PHE CYS PRO GLU GLY GLU VAL LEU ASP VAL PHE LEU SEQRES 8 A 178 ASP ILE ARG LYS ASP SER ASN THR TYR GLY GLN PHE MET SEQRES 9 A 178 SER PHE ILE LEU ASN PRO HIS ASN ARG ARG SER ILE PHE SEQRES 10 A 178 LEU ALA LYS GLY ILE ALA HIS GLY PHE LEU SER MET LYS SEQRES 11 A 178 ASP ASN THR LEU ILE VAL CYS LYS THR SER THR VAL HIS SEQRES 12 A 178 SER PRO SER ARG ASP SER GLY ILE HIS TRP ASN SER PHE SEQRES 13 A 178 GLY PHE LYS TRP PRO VAL GLU ASN PRO ILE ILE SER ASP SEQRES 14 A 178 LYS ASP ARG ASN LEU ASP CYS PHE PHE SEQRES 1 B 178 GLY HIS MET ALA SER ILE ILE ASN ILE THR GLU LEU ASN SEQRES 2 B 178 ILE SER GLY CYS TYR LEU ILE GLU SER PRO ILE PHE SER SEQRES 3 B 178 ASP GLU ARG GLY GLU PHE VAL LYS THR HIS HIS GLN GLU SEQRES 4 B 178 ILE PHE LYS ASN PHE GLY LEU GLU ILE PRO SER ALA GLU SEQRES 5 B 178 GLU TYR TYR SER ARG SER LYS ASN ASN VAL ILE ARG GLY SEQRES 6 B 178 MET HIS PHE GLN GLN TYR PRO ASP ASP HIS ASN LYS LEU SEQRES 7 B 178 VAL PHE CYS PRO GLU GLY GLU VAL LEU ASP VAL PHE LEU SEQRES 8 B 178 ASP ILE ARG LYS ASP SER ASN THR TYR GLY GLN PHE MET SEQRES 9 B 178 SER PHE ILE LEU ASN PRO HIS ASN ARG ARG SER ILE PHE SEQRES 10 B 178 LEU ALA LYS GLY ILE ALA HIS GLY PHE LEU SER MET LYS SEQRES 11 B 178 ASP ASN THR LEU ILE VAL CYS LYS THR SER THR VAL HIS SEQRES 12 B 178 SER PRO SER ARG ASP SER GLY ILE HIS TRP ASN SER PHE SEQRES 13 B 178 GLY PHE LYS TRP PRO VAL GLU ASN PRO ILE ILE SER ASP SEQRES 14 B 178 LYS ASP ARG ASN LEU ASP CYS PHE PHE SEQRES 1 C 178 GLY HIS MET ALA SER ILE ILE ASN ILE THR GLU LEU ASN SEQRES 2 C 178 ILE SER GLY CYS TYR LEU ILE GLU SER PRO ILE PHE SER SEQRES 3 C 178 ASP GLU ARG GLY GLU PHE VAL LYS THR HIS HIS GLN GLU SEQRES 4 C 178 ILE PHE LYS ASN PHE GLY LEU GLU ILE PRO SER ALA GLU SEQRES 5 C 178 GLU TYR TYR SER ARG SER LYS ASN ASN VAL ILE ARG GLY SEQRES 6 C 178 MET HIS PHE GLN GLN TYR PRO ASP ASP HIS ASN LYS LEU SEQRES 7 C 178 VAL PHE CYS PRO GLU GLY GLU VAL LEU ASP VAL PHE LEU SEQRES 8 C 178 ASP ILE ARG LYS ASP SER ASN THR TYR GLY GLN PHE MET SEQRES 9 C 178 SER PHE ILE LEU ASN PRO HIS ASN ARG ARG SER ILE PHE SEQRES 10 C 178 LEU ALA LYS GLY ILE ALA HIS GLY PHE LEU SER MET LYS SEQRES 11 C 178 ASP ASN THR LEU ILE VAL CYS LYS THR SER THR VAL HIS SEQRES 12 C 178 SER PRO SER ARG ASP SER GLY ILE HIS TRP ASN SER PHE SEQRES 13 C 178 GLY PHE LYS TRP PRO VAL GLU ASN PRO ILE ILE SER ASP SEQRES 14 C 178 LYS ASP ARG ASN LEU ASP CYS PHE PHE HET PO4 A 201 5 HET PO4 A 202 5 HET CYT A 203 8 HET EDO A 204 4 HET PO4 B 201 5 HET PO4 B 202 5 HET CYT B 203 8 HET PO4 C 201 5 HETNAM PO4 PHOSPHATE ION HETNAM CYT 6-AMINOPYRIMIDIN-2(1H)-ONE HETNAM EDO 1,2-ETHANEDIOL HETSYN CYT CYTOSINE HETSYN EDO ETHYLENE GLYCOL FORMUL 4 PO4 5(O4 P 3-) FORMUL 6 CYT 2(C4 H5 N3 O) FORMUL 7 EDO C2 H6 O2 FORMUL 12 HOH *400(H2 O) HELIX 1 AA1 GLN A 34 ASN A 39 1 6 HELIX 2 AA2 SER A 164 ASN A 169 1 6 HELIX 3 AA3 HIS B 33 ASN B 39 1 7 HELIX 4 AA4 SER B 164 ASN B 169 1 6 HELIX 5 AA5 GLN C 34 PHE C 40 1 7 HELIX 6 AA6 SER C 164 ASN C 169 1 6 SHEET 1 AA1 8 ASN A 4 GLU A 7 0 SHEET 2 AA1 8 TYR A 14 GLU A 17 -1 O GLU A 17 N ASN A 4 SHEET 3 AA1 8 ARG A 110 LEU A 114 -1 O SER A 111 N ILE A 16 SHEET 4 AA1 8 LYS A 73 GLU A 79 -1 N LYS A 73 O LEU A 114 SHEET 5 AA1 8 THR A 129 THR A 135 -1 O LYS A 134 N LEU A 74 SHEET 6 AA1 8 GLU A 48 SER A 54 -1 N TYR A 50 O CYS A 133 SHEET 7 AA1 8 GLY C 26 HIS C 33 -1 O VAL C 29 N TYR A 51 SHEET 8 AA1 8 ILE C 20 ASP C 23 -1 N ASP C 23 O GLY C 26 SHEET 1 AA2 8 ILE A 20 ASP A 23 0 SHEET 2 AA2 8 GLY A 26 HIS A 33 -1 O GLY A 26 N ASP A 23 SHEET 3 AA2 8 GLU C 48 SER C 54 -1 O TYR C 51 N VAL A 29 SHEET 4 AA2 8 THR C 129 THR C 135 -1 O CYS C 133 N TYR C 50 SHEET 5 AA2 8 LYS C 73 GLU C 79 -1 N GLU C 79 O LEU C 130 SHEET 6 AA2 8 ARG C 110 LEU C 114 -1 O LEU C 114 N LYS C 73 SHEET 7 AA2 8 TYR C 14 GLU C 17 -1 N ILE C 16 O SER C 111 SHEET 8 AA2 8 ASN C 4 GLU C 7 -1 N ASN C 4 O GLU C 17 SHEET 1 AA3 5 PHE A 99 LEU A 104 0 SHEET 2 AA3 5 VAL A 82 ASP A 88 -1 N ASP A 84 O PHE A 102 SHEET 3 AA3 5 ILE A 118 SER A 124 -1 O GLY A 121 N VAL A 85 SHEET 4 AA3 5 ILE A 59 GLN A 65 -1 N HIS A 63 O HIS A 120 SHEET 5 AA3 5 ASP A 144 GLY A 146 -1 O SER A 145 N PHE A 64 SHEET 1 AA4 6 ASN B 4 GLU B 7 0 SHEET 2 AA4 6 TYR B 14 GLU B 17 -1 O LEU B 15 N THR B 6 SHEET 3 AA4 6 ARG B 110 LEU B 114 -1 O PHE B 113 N TYR B 14 SHEET 4 AA4 6 LYS B 73 GLU B 79 -1 N LYS B 73 O LEU B 114 SHEET 5 AA4 6 THR B 129 THR B 135 -1 O VAL B 132 N PHE B 76 SHEET 6 AA4 6 GLU B 48 SER B 54 -1 N TYR B 50 O CYS B 133 SHEET 1 AA5 2 ILE B 20 ASP B 23 0 SHEET 2 AA5 2 GLY B 26 VAL B 29 -1 O GLY B 26 N ASP B 23 SHEET 1 AA6 5 PHE B 99 LEU B 104 0 SHEET 2 AA6 5 VAL B 82 ASP B 88 -1 N ASP B 84 O PHE B 102 SHEET 3 AA6 5 ILE B 118 SER B 124 -1 O ALA B 119 N LEU B 87 SHEET 4 AA6 5 ILE B 59 GLN B 65 -1 N HIS B 63 O HIS B 120 SHEET 5 AA6 5 ASP B 144 GLY B 146 -1 O SER B 145 N PHE B 64 SHEET 1 AA7 5 PHE C 99 LEU C 104 0 SHEET 2 AA7 5 VAL C 82 ASP C 88 -1 N ASP C 84 O PHE C 102 SHEET 3 AA7 5 ILE C 118 SER C 124 -1 O ALA C 119 N LEU C 87 SHEET 4 AA7 5 ILE C 59 GLN C 65 -1 N HIS C 63 O HIS C 120 SHEET 5 AA7 5 ASP C 144 GLY C 146 -1 O SER C 145 N PHE C 64 CISPEP 1 GLY A 61 MET A 62 0 -4.51 CISPEP 2 TYR A 67 PRO A 68 0 5.23 CISPEP 3 GLY B 61 MET B 62 0 -6.01 CISPEP 4 TYR B 67 PRO B 68 0 4.25 CISPEP 5 GLY C 61 MET C 62 0 -5.67 CISPEP 6 TYR C 67 PRO C 68 0 7.33 SITE 1 AC1 6 ARG A 60 HIS A 63 PO4 A 202 ARG C 25 SITE 2 AC1 6 PHE C 28 HOH C 327 SITE 1 AC2 7 TYR A 50 HIS A 63 LYS A 73 HIS A 120 SITE 2 AC2 7 PO4 A 201 HOH A 303 HOH A 304 SITE 1 AC3 7 GLU A 48 HIS A 139 HOH A 339 HOH A 416 SITE 2 AC3 7 HOH A 451 PHE C 28 LYS C 30 SITE 1 AC4 3 GLU A 7 GLY A 12 HOH A 306 SITE 1 AC5 5 ARG B 25 PHE B 28 ARG B 60 HIS B 63 SITE 2 AC5 5 PO4 B 202 SITE 1 AC6 6 TYR B 50 HIS B 63 LYS B 73 HIS B 120 SITE 2 AC6 6 PO4 B 201 HOH B 301 SITE 1 AC7 7 PHE B 28 LYS B 30 GLU B 48 HIS B 139 SITE 2 AC7 7 HOH B 319 HOH B 359 HOH B 380 SITE 1 AC8 4 ARG A 25 ARG C 60 HIS C 63 HOH C 333 CRYST1 79.160 42.678 150.463 90.00 90.39 90.00 C 1 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 0.012633 0.000000 0.000086 0.00000 SCALE2 0.000000 0.023431 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006646 0.00000