PDB Short entry for 2OPF HEADER HYDROLASE/DNA 29-JAN-07 2OPF TITLE CRYSTAL STRUCTURE OF THE DNA REPAIR ENZYME ENDONUCLEASE-VIII (NEI) TITLE 2 FROM E. COLI (R252A) IN COMPLEX WITH AP-SITE CONTAINING DNA SUBSTRATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*GP*CP*TP*TP*CP*AP*TP*CP*CP*TP*G)-3'; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(P*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3'; COMPND 7 CHAIN: C; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: ENDONUCLEASE VIII; COMPND 11 CHAIN: A; COMPND 12 SYNONYM: DNA GLYCOSYLASE/AP LYASE NEI, DNA-APURINIC OR APYRIMIDINIC COMPND 13 SITE, LYASE NEI; COMPND 14 EC: 3.2.2.-, 4.2.99.18; COMPND 15 ENGINEERED: YES; COMPND 16 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 7 ORGANISM_TAXID: 562; SOURCE 8 GENE: NEI; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 11 EXPRESSION_SYSTEM_STRAIN: B834(DE3); SOURCE 12 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 13 EXPRESSION_SYSTEM_PLASMID: PET13A KEYWDS ENDONUCLEASE VIII, OXIDATIVE DAMAGE, DNA REPAIR, BASE EXCISION, KEYWDS 2 COVALENT INTERMEDIATE, REACTION MECHANISM, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR G.GOLAN,D.O.ZHAROV,A.P.GROLLMAN,G.SHOHAM REVDAT 5 25-OCT-23 2OPF 1 REMARK REVDAT 4 10-NOV-21 2OPF 1 REMARK SEQADV LINK REVDAT 3 13-JUL-11 2OPF 1 VERSN REVDAT 2 24-FEB-09 2OPF 1 VERSN REVDAT 1 26-FEB-08 2OPF 0 JRNL AUTH G.GOLAN,D.O.ZHARKOV,A.P.GROLLMAN,G.SHOHAM JRNL TITL ACTIVE SITE PLASTICITY OF ENDONUCLEASE VIII: CONFORMATIONAL JRNL TITL 2 CHANGES COMPENSATING FOR DIFFERENT SUBSTRATES AND MUTATIONS JRNL TITL 3 OF CRITICAL RESIDUES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.41 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1090137.800 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 89.4 REMARK 3 NUMBER OF REFLECTIONS : 36395 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) : 0.240 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1831 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 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) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.97 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 84.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 5308 REMARK 3 BIN R VALUE (WORKING SET) : 0.2990 REMARK 3 BIN FREE R VALUE : 0.3390 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 282 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2039 REMARK 3 NUCLEIC ACID ATOMS : 461 REMARK 3 HETEROGEN ATOMS : 36 REMARK 3 SOLVENT ATOMS : 243 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.97000 REMARK 3 B22 (A**2) : 2.97000 REMARK 3 B33 (A**2) : -5.93000 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) : 0.25 REMARK 3 ESD FROM SIGMAA (A) : 0.16 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) : 0.29 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.17 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.910 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) : 1.310 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.980 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.860 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.740 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.45 REMARK 3 BSOL : 71.16 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 : DNA-RNA-PED.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 5 : GOL.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA-PED.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : WATER.TOP REMARK 3 TOPOLOGY FILE 5 : GOL.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2OPF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-FEB-07. REMARK 100 THE DEPOSITION ID IS D_1000041423. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-DEC-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 5ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.102 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39078 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 13.00 REMARK 200 R MERGE (I) : 0.09900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.88 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.49100 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: CNS REMARK 200 STARTING MODEL: 2EA0 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.8M AMMONIUM SULFATE, 0.1M SODIUM REMARK 280 ACETATE PH 4.6-5.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 2 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,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z+1/2 REMARK 290 7555 Y,X,-Z+1/4 REMARK 290 8555 -Y,-X,-Z+3/4 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 85.05650 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 127.58475 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 42.52825 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 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 85.05650 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 42.52825 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 127.58475 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C, 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 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 DG B 401 REMARK 465 GLU A 217 REMARK 465 ASN A 218 REMARK 465 LYS A 219 REMARK 465 HIS A 220 REMARK 465 HIS A 221 REMARK 465 GLY A 222 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 PRO A 83 CG CD REMARK 470 GLU A 109 CG CD OE1 OE2 REMARK 470 GLU A 114 CG CD OE1 OE2 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 CG GLU A 137 CG GLU A 137 7555 2.05 REMARK 500 O HOH C 1076 O HOH C 1076 5655 2.09 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 PED C 427 O3' DG C 428 P 0.148 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 PED C 427 C3' - O3' - P ANGL. DEV. = 9.9 DEGREES REMARK 500 DG C 428 O3' - P - O5' ANGL. DEV. = -13.3 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 GLN A 69 -122.92 47.94 REMARK 500 SER A 104 -35.12 66.43 REMARK 500 PHE A 162 -70.42 -87.98 REMARK 500 GLN A 214 -62.35 82.76 REMARK 500 VAL A 215 146.17 64.92 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 ZN A 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 237 SG REMARK 620 2 CYS A 240 SG 118.0 REMARK 620 3 CYS A 257 SG 108.7 96.2 REMARK 620 4 CYS A 260 SG 99.8 119.9 114.5 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL C 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 703 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 704 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 705 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2EA0 RELATED DB: PDB REMARK 900 RELATED ID: 2OQ4 RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 SEQUENCING AND CRYSTALLOGRAPHY CONFIRM THE SEQUENCE AS THR A 34 AND REMARK 999 ARG A 112. DBREF 2OPF A 1 262 UNP P50465 END8_ECOLI 2 263 DBREF 2OPF B 401 412 PDB 2OPF 2OPF 401 412 DBREF 2OPF C 422 433 PDB 2OPF 2OPF 422 433 SEQADV 2OPF THR A 34 UNP P50465 PRO 35 SEE REMARK 999 SEQADV 2OPF ARG A 112 UNP P50465 THR 113 SEE REMARK 999 SEQADV 2OPF ALA A 252 UNP P50465 ARG 253 ENGINEERED MUTATION SEQRES 1 B 12 DG DG DC DT DT DC DA DT DC DC DT DG SEQRES 1 C 12 DC DA DG DG DA PED DG DA DA DG DC DC SEQRES 1 A 262 PRO GLU GLY PRO GLU ILE ARG ARG ALA ALA ASP ASN LEU SEQRES 2 A 262 GLU ALA ALA ILE LYS GLY LYS PRO LEU THR ASP VAL TRP SEQRES 3 A 262 PHE ALA PHE PRO GLN LEU LYS THR TYR GLN SER GLN LEU SEQRES 4 A 262 ILE GLY GLN HIS VAL THR HIS VAL GLU THR ARG GLY LYS SEQRES 5 A 262 ALA LEU LEU THR HIS PHE SER ASN ASP LEU THR LEU TYR SEQRES 6 A 262 SER HIS ASN GLN LEU TYR GLY VAL TRP ARG VAL VAL ASP SEQRES 7 A 262 THR GLY GLU GLU PRO GLN THR THR ARG VAL LEU ARG VAL SEQRES 8 A 262 LYS LEU GLN THR ALA ASP LYS THR ILE LEU LEU TYR SER SEQRES 9 A 262 ALA SER ASP ILE GLU MET LEU ARG PRO GLU GLN LEU THR SEQRES 10 A 262 THR HIS PRO PHE LEU GLN ARG VAL GLY PRO ASP VAL LEU SEQRES 11 A 262 ASP PRO ASN LEU THR PRO GLU VAL VAL LYS GLU ARG LEU SEQRES 12 A 262 LEU SER PRO ARG PHE ARG ASN ARG GLN PHE ALA GLY LEU SEQRES 13 A 262 LEU LEU ASP GLN ALA PHE LEU ALA GLY LEU GLY ASN TYR SEQRES 14 A 262 LEU ARG VAL GLU ILE LEU TRP GLN VAL GLY LEU THR GLY SEQRES 15 A 262 ASN HIS LYS ALA LYS ASP LEU ASN ALA ALA GLN LEU ASP SEQRES 16 A 262 ALA LEU ALA HIS ALA LEU LEU GLU ILE PRO ARG PHE SER SEQRES 17 A 262 TYR ALA THR ARG GLY GLN VAL ASP GLU ASN LYS HIS HIS SEQRES 18 A 262 GLY ALA LEU PHE ARG PHE LYS VAL PHE HIS ARG ASP GLY SEQRES 19 A 262 GLU PRO CYS GLU ARG CYS GLY SER ILE ILE GLU LYS THR SEQRES 20 A 262 THR LEU SER SER ALA PRO PHE TYR TRP CYS PRO GLY CYS SEQRES 21 A 262 GLN HIS HET PED C 427 11 HET GOL C 702 6 HET ZN A 501 1 HET SO4 A 601 5 HET GOL A 701 6 HET GOL A 703 6 HET GOL A 704 6 HET GOL A 705 6 HETNAM PED PENTANE-3,4-DIOL-5-PHOSPHATE HETNAM GOL GLYCEROL HETNAM ZN ZINC ION HETNAM SO4 SULFATE ION HETSYN PED OPEN FORM OF 1'-2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 PED C5 H13 O6 P FORMUL 4 GOL 5(C3 H8 O3) FORMUL 5 ZN ZN 2+ FORMUL 6 SO4 O4 S 2- FORMUL 11 HOH *243(H2 O) HELIX 1 1 GLU A 2 LYS A 18 1 17 HELIX 2 2 PHE A 29 LYS A 33 5 5 HELIX 3 3 THR A 34 ILE A 40 1 7 HELIX 4 4 ARG A 112 THR A 118 1 7 HELIX 5 5 HIS A 119 VAL A 125 1 7 HELIX 6 6 THR A 135 SER A 145 1 11 HELIX 7 7 GLN A 152 LEU A 157 1 6 HELIX 8 8 GLY A 167 VAL A 178 1 12 HELIX 9 9 LYS A 185 LEU A 189 5 5 HELIX 10 10 ASN A 190 ARG A 212 1 23 SHEET 1 A 4 LEU A 22 PHE A 27 0 SHEET 2 A 4 LEU A 89 THR A 95 -1 O LYS A 92 N TRP A 26 SHEET 3 A 4 LYS A 98 TYR A 103 -1 O LEU A 102 N ARG A 90 SHEET 4 A 4 VAL A 73 ASP A 78 -1 N VAL A 73 O TYR A 103 SHEET 1 B 4 VAL A 44 ARG A 50 0 SHEET 2 B 4 ALA A 53 PHE A 58 -1 O LEU A 55 N GLU A 48 SHEET 3 B 4 THR A 63 HIS A 67 -1 O SER A 66 N LEU A 54 SHEET 4 B 4 ASP A 107 LEU A 111 -1 O LEU A 111 N THR A 63 SHEET 1 C 2 GLU A 245 LEU A 249 0 SHEET 2 C 2 ALA A 252 TRP A 256 -1 O PHE A 254 N THR A 247 LINK O3' DA C 426 P PED C 427 1555 1555 1.61 LINK C1' PED C 427 N PRO A 1 1555 1555 1.51 LINK SG CYS A 237 ZN ZN A 501 1555 1555 2.34 LINK SG CYS A 240 ZN ZN A 501 1555 1555 2.36 LINK SG CYS A 257 ZN ZN A 501 1555 1555 2.21 LINK SG CYS A 260 ZN ZN A 501 1555 1555 2.33 SITE 1 AC2 4 CYS A 237 CYS A 240 CYS A 257 CYS A 260 SITE 1 AC3 5 ARG A 8 ASN A 12 GLY A 213 GLN A 214 SITE 2 AC3 5 HOH A1220 SITE 1 AC4 7 GLN A 177 ALA A 196 ALA A 200 GLU A 203 SITE 2 AC4 7 HOH A1137 HOH A1166 HOH A1176 SITE 1 AC5 8 DA B 407 DG C 424 DG C 425 DA C 426 SITE 2 AC5 8 HOH C1050 HOH C1070 HOH C1134 HOH C1163 SITE 1 AC6 6 ALA A 9 ASN A 12 ASN A 68 TRP A 74 SITE 2 AC6 6 HOH A1039 HOH A1153 SITE 1 AC7 7 ASP A 24 TRP A 26 GLN A 36 GLY A 80 SITE 2 AC7 7 GLU A 82 LYS A 92 HOH A1123 SITE 1 AC8 2 ARG A 75 GLN A 84 CRYST1 73.556 73.556 170.113 90.00 90.00 90.00 P 43 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 0.013595 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013595 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005878 0.00000