PDB Short entry for 6FBU HEADER HYDROLASE 19-DEC-17 6FBU TITLE CRYSTAL STRUCTURE OF THE DNA REPAIR ENZYME ENDONUCLEASE-VIII (NEI) TITLE 2 FROM E. COLI (E2Q) IN COMPLEX WITH AP-SITE CONTAINING DNA SUBSTRATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDONUCLEASE 8; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DNA GLYCOSYLASE/AP LYASE NEI,DNA-(APURINIC OR APYRIMIDINIC COMPND 5 SITE) LYASE NEI,ENDONUCLEASE VIII; COMPND 6 EC: 3.2.2.-,4.2.99.18; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: DNA (5'-D(P*GP*GP*CP*TP*TP*CP*AP*TP*CP*CP*TP*G)-3'); COMPND 11 CHAIN: B; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: DNA (5'-D(P*CP*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3'); COMPND 15 CHAIN: C; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: NEI, B0714, JW0704; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 15 ORGANISM_TAXID: 32630 KEYWDS ENDONUCLEASE-VIII, NEI, DNA REPAIR ENZYME, COVALENT INTERMEDIATE, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.POMYALOV,S.LANSKY,G.GOLAN,D.O.ZHARKOV,A.P.GROLLMAN,G.SHOHAM REVDAT 2 17-JAN-24 6FBU 1 REMARK REVDAT 1 30-JAN-19 6FBU 0 JRNL AUTH S.POMYALOV,S.LANSKY,G.GOLAN,D.O.ZHARKOV,A.P.GROLLMAN, JRNL AUTH 2 G.SHOHAM JRNL TITL CRYSTAL STRUCTURE OF THE DNA REPAIR ENZYME ENDONUCLEASE-VIII JRNL TITL 2 (NEI) FROM E. COLI (E2Q) IN COMPLEX WITH AP-SITE CONTAINING JRNL TITL 3 DNA SUBSTRATE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.12_2829 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.25 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 32770 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.243 REMARK 3 R VALUE (WORKING SET) : 0.241 REMARK 3 FREE R VALUE : 0.281 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1999 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 20.2523 - 4.8003 0.99 2372 154 0.2178 0.2255 REMARK 3 2 4.8003 - 3.8185 1.00 2264 148 0.2114 0.2450 REMARK 3 3 3.8185 - 3.3383 1.00 2233 143 0.2204 0.2699 REMARK 3 4 3.3383 - 3.0342 1.00 2209 144 0.2597 0.3324 REMARK 3 5 3.0342 - 2.8173 1.00 2194 142 0.2678 0.3141 REMARK 3 6 2.8173 - 2.6516 1.00 2182 143 0.2685 0.3357 REMARK 3 7 2.6516 - 2.5190 1.00 2175 141 0.2712 0.3207 REMARK 3 8 2.5190 - 2.4096 1.00 2186 143 0.2813 0.3481 REMARK 3 9 2.4096 - 2.3169 1.00 2157 139 0.2660 0.3093 REMARK 3 10 2.3169 - 2.2371 1.00 2180 142 0.2524 0.3110 REMARK 3 11 2.2371 - 2.1672 1.00 2153 141 0.2562 0.3061 REMARK 3 12 2.1672 - 2.1053 1.00 2140 138 0.2523 0.2937 REMARK 3 13 2.1053 - 2.0500 1.00 2167 141 0.2748 0.2833 REMARK 3 14 2.0500 - 2.0000 1.00 2159 140 0.2804 0.3143 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.060 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.58 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.009 2692 REMARK 3 ANGLE : 1.065 3743 REMARK 3 CHIRALITY : 0.355 416 REMARK 3 PLANARITY : 0.006 400 REMARK 3 DIHEDRAL : 14.028 1997 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6FBU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-DEC-17. REMARK 100 THE DEPOSITION ID IS D_1200008056. 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 : 4.6-5.0 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 : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS, POINTLESS 1.10.25 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32845 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 20.730 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.10700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : 0.79200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.900 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: 2OQ4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.8M AMMONIUM SULFATE, 0.1M SODIUM REMARK 280 ACETATE PH, PH 4.6, 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 82.19000 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 123.28500 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 41.09500 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 82.19000 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 41.09500 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 123.28500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4080 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14590 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -54.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 590 LIES ON A SPECIAL POSITION. 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 VAL A 215 REMARK 465 ASP A 216 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 465 DG B 413 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 N PRO A 1 C1' PED C 427 1.62 REMARK 500 O HOH A 508 O HOH A 536 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 OP1 DG B 401 OP2 DC C 433 5657 2.18 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 DG B 402 O3' - P - O5' ANGL. DEV. = 18.3 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 2 -163.82 -121.17 REMARK 500 ASP A 61 -3.21 71.49 REMARK 500 GLN A 69 -127.91 50.59 REMARK 500 SER A 104 -29.83 56.32 REMARK 500 VAL A 229 -31.19 -133.80 REMARK 500 THR A 247 -158.89 -136.93 REMARK 500 CYS A 260 16.82 -140.53 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 A 588 DISTANCE = 6.07 ANGSTROMS REMARK 525 HOH A 590 DISTANCE = 6.34 ANGSTROMS REMARK 525 HOH A 591 DISTANCE = 7.40 ANGSTROMS 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 304 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 237 SG REMARK 620 2 CYS A 240 SG 115.7 REMARK 620 3 CYS A 257 SG 112.7 92.4 REMARK 620 4 CYS A 260 SG 107.8 115.5 112.4 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 SO4 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 305 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2EA0 RELATED DB: PDB REMARK 900 CONTAINS THE WT ENZYME IN COMPLEX WITH DNA REMARK 900 RELATED ID: 2OPF RELATED DB: PDB REMARK 900 CONTAINS A DIFFERENT MUTANT (R252A) IN COMPLEX WITH DNA REMARK 900 RELATED ID: 2OQ4 RELATED DB: PDB REMARK 900 PREVIOUS PROCESSING OF SAME MUTANT, (E2Q) DBREF 6FBU A 1 262 UNP P50465 END8_ECOLI 2 263 DBREF 6FBU B 401 413 PDB 6FBU 6FBU 401 413 DBREF 6FBU C 421 433 PDB 6FBU 6FBU 421 433 SEQADV 6FBU GLN A 2 UNP P50465 GLU 3 ENGINEERED MUTATION SEQADV 6FBU THR A 34 UNP P50465 PRO 35 ENGINEERED MUTATION SEQADV 6FBU ARG A 112 UNP P50465 THR 113 ENGINEERED MUTATION SEQRES 1 A 262 PRO GLN 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 ARG PRO PHE TYR TRP CYS PRO GLY CYS SEQRES 21 A 262 GLN HIS SEQRES 1 B 13 DG DG DC DT DT DC DA DT DC DC DT DG DG SEQRES 1 C 13 DC DC DA DG DG DA PED DG DA DA DG DC DC HET PED C 427 11 HET SO4 A 301 5 HET SO4 A 302 5 HET SO4 A 303 5 HET ZN A 304 1 HET ACT A 305 4 HETNAM PED PENTANE-3,4-DIOL-5-PHOSPHATE HETNAM SO4 SULFATE ION HETNAM ZN ZINC ION HETNAM ACT ACETATE ION HETSYN PED OPEN FORM OF 1'-2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE FORMUL 3 PED C5 H13 O6 P FORMUL 4 SO4 3(O4 S 2-) FORMUL 7 ZN ZN 2+ FORMUL 8 ACT C2 H3 O2 1- FORMUL 9 HOH *205(H2 O) HELIX 1 AA1 GLN A 2 LYS A 18 1 17 HELIX 2 AA2 PHE A 29 LYS A 33 5 5 HELIX 3 AA3 THR A 34 ILE A 40 1 7 HELIX 4 AA4 GLU A 114 HIS A 119 1 6 HELIX 5 AA5 HIS A 119 VAL A 125 1 7 HELIX 6 AA6 THR A 135 SER A 145 1 11 HELIX 7 AA7 GLN A 152 LEU A 157 1 6 HELIX 8 AA8 GLY A 167 VAL A 178 1 12 HELIX 9 AA9 LYS A 185 LEU A 189 5 5 HELIX 10 AB1 ASN A 190 ARG A 212 1 23 SHEET 1 AA1 4 ASP A 24 PHE A 27 0 SHEET 2 AA1 4 LEU A 89 GLN A 94 -1 O GLN A 94 N ASP A 24 SHEET 3 AA1 4 LYS A 98 TYR A 103 -1 O LEU A 102 N ARG A 90 SHEET 4 AA1 4 VAL A 73 ASP A 78 -1 N VAL A 77 O THR A 99 SHEET 1 AA2 4 VAL A 44 ARG A 50 0 SHEET 2 AA2 4 ALA A 53 PHE A 58 -1 O LEU A 55 N GLU A 48 SHEET 3 AA2 4 THR A 63 HIS A 67 -1 O LEU A 64 N THR A 56 SHEET 4 AA2 4 ASP A 107 LEU A 111 -1 O LEU A 111 N THR A 63 SHEET 1 AA3 2 GLU A 245 LEU A 249 0 SHEET 2 AA3 2 ARG A 252 TRP A 256 -1 O TRP A 256 N GLU A 245 LINK O3' DA C 426 P PED C 427 1555 1555 1.57 LINK O3' PED C 427 P DG C 428 1555 1555 1.58 LINK SG CYS A 237 ZN ZN A 304 1555 1555 2.24 LINK SG CYS A 240 ZN ZN A 304 1555 1555 2.49 LINK SG CYS A 257 ZN ZN A 304 1555 1555 2.15 LINK SG CYS A 260 ZN ZN A 304 1555 1555 2.40 SITE 1 AC1 4 ARG A 8 ASN A 12 ACT A 305 HOH A 455 SITE 1 AC2 6 PRO A 1 GLU A 5 ARG A 212 HOH A 493 SITE 2 AC2 6 HOH A 502 PED C 427 SITE 1 AC3 1 ARG A 149 SITE 1 AC4 4 CYS A 237 CYS A 240 CYS A 257 CYS A 260 SITE 1 AC5 2 GLU A 5 SO4 A 301 CRYST1 75.340 75.340 164.380 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 0.013273 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013273 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006083 0.00000