PDB Short entry for 5C5J HEADER TRANSFERASE/DNA 20-JUN-15 5C5J TITLE POYMERASE NUCLEOTIDE COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE IV; COMPND 3 CHAIN: F, A; COMPND 4 SYNONYM: POL IV; COMPND 5 EC: 2.7.7.7; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'- COMPND 9 D(*TP*CP*TP*AP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3'); COMPND 10 CHAIN: G, H, B, C; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 STRAIN: [NUMBER SIGN]1/H766; SOURCE 5 GENE: DINB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: C41DE3; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX6P1; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 14 ORGANISM_TAXID: 562 KEYWDS DNA POLYMERASE, REPLICATION, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR D.T.NAIR,J.KOTTUR REVDAT 2 08-NOV-23 5C5J 1 JRNL REMARK REVDAT 1 22-JUN-16 5C5J 0 JRNL AUTH J.KOTTUR,D.T.NAIR JRNL TITL REACTIVE OXYGEN SPECIES PLAY AN IMPORTANT ROLE IN THE JRNL TITL 2 BACTERICIDAL ACTIVITY OF QUINOLONE ANTIBIOTICS JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 55 2397 2016 JRNL REFN ESSN 1521-3773 JRNL PMID 26757158 JRNL DOI 10.1002/ANIE.201509340 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.91 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.690 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 61592 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.225 REMARK 3 R VALUE (WORKING SET) : 0.222 REMARK 3 FREE R VALUE : 0.274 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 3136 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 36.9146 - 6.5136 0.93 3668 170 0.1635 0.1724 REMARK 3 2 6.5136 - 5.1746 1.00 3919 195 0.1845 0.2257 REMARK 3 3 5.1746 - 4.5218 1.00 3935 196 0.1772 0.2006 REMARK 3 4 4.5218 - 4.1090 1.00 3887 199 0.1687 0.2290 REMARK 3 5 4.1090 - 3.8148 1.00 3908 240 0.1859 0.2439 REMARK 3 6 3.8148 - 3.5901 1.00 3892 214 0.1936 0.2202 REMARK 3 7 3.5901 - 3.4104 1.00 3963 203 0.2058 0.2712 REMARK 3 8 3.4104 - 3.2621 1.00 3886 222 0.2150 0.2765 REMARK 3 9 3.2621 - 3.1365 1.00 3902 228 0.2306 0.3157 REMARK 3 10 3.1365 - 3.0284 1.00 3885 236 0.2470 0.2850 REMARK 3 11 3.0284 - 2.9337 1.00 3940 189 0.2644 0.3401 REMARK 3 12 2.9337 - 2.8499 1.00 3904 232 0.2829 0.3716 REMARK 3 13 2.8499 - 2.7749 1.00 3891 228 0.2743 0.3232 REMARK 3 14 2.7749 - 2.7072 1.00 3851 237 0.2692 0.3172 REMARK 3 15 2.7072 - 2.6457 1.00 3907 217 0.2776 0.3576 REMARK 3 16 2.6457 - 2.5894 1.00 3939 221 0.2773 0.3329 REMARK 3 17 2.5894 - 2.5376 1.00 3912 180 0.2840 0.4443 REMARK 3 18 2.5376 - 2.4897 1.00 3928 187 0.2896 0.3520 REMARK 3 19 2.4897 - 2.4453 1.00 3948 196 0.2816 0.3291 REMARK 3 20 2.4453 - 2.4038 1.00 3846 211 0.2889 0.3279 REMARK 3 21 2.4038 - 2.3651 1.00 4016 165 0.2872 0.3539 REMARK 3 22 2.3651 - 2.3287 1.00 3953 214 0.2982 0.3647 REMARK 3 23 2.3287 - 2.2944 1.00 3814 243 0.2993 0.3650 REMARK 3 24 2.2944 - 2.2621 1.00 3922 205 0.2908 0.3326 REMARK 3 25 2.2621 - 2.2316 0.99 3949 204 0.3234 0.3554 REMARK 3 26 2.2316 - 2.2026 1.00 3845 205 0.2973 0.3326 REMARK 3 27 2.2026 - 2.1751 1.00 3934 198 0.2915 0.3176 REMARK 3 28 2.1751 - 2.1489 0.99 3921 194 0.3055 0.3509 REMARK 3 29 2.1489 - 2.1239 0.99 3770 218 0.3083 0.3565 REMARK 3 30 2.1239 - 2.1000 0.97 3878 224 0.3247 0.4257 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.330 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.320 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 7027 REMARK 3 ANGLE : 1.078 9785 REMARK 3 CHIRALITY : 0.061 1097 REMARK 3 PLANARITY : 0.006 1032 REMARK 3 DIHEDRAL : 18.414 4017 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 5C5J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-JUN-15. REMARK 100 THE DEPOSITION ID IS D_1000210858. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-NOV-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5-6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM14 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91596 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SCALA REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 63454 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 36.909 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : 0.07800 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.60600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.400 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: 4IR9 REMARK 200 REMARK 200 REMARK: ROD SHAPED REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MPD, PH 5.5, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 28.69000 REMARK 290 SMTRY3 2 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -39.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: F, G, H 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5450 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -46.0 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 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 GLN F 342 REMARK 465 MET F 343 REMARK 465 GLU F 344 REMARK 465 ARG F 345 REMARK 465 GLN F 346 REMARK 465 LEU F 347 REMARK 465 VAL F 348 REMARK 465 LEU F 349 REMARK 465 GLY F 350 REMARK 465 LEU F 351 REMARK 465 GLN A 342 REMARK 465 MET A 343 REMARK 465 GLU A 344 REMARK 465 ARG A 345 REMARK 465 GLN A 346 REMARK 465 LEU A 347 REMARK 465 VAL A 348 REMARK 465 LEU A 349 REMARK 465 GLY A 350 REMARK 465 LEU A 351 REMARK 465 DT H 856 REMARK 465 DC H 857 REMARK 465 DT H 858 REMARK 465 DA H 859 REMARK 465 DT C 856 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 LYS F 64 CG CD CE NZ REMARK 470 LYS F 205 CG CD CE NZ REMARK 470 LYS A 64 CG CD CE NZ REMARK 470 LYS A 205 CG CD CE NZ REMARK 470 DG H 860 P OP1 OP2 REMARK 470 DC H 873 O3' REMARK 470 DC C 857 P OP1 OP2 REMARK 470 DC C 873 O3' 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 NH2 ARG A 240 OP1 DG B 843 2.01 REMARK 500 OE1 GLU F 81 O HOH F 401 2.03 REMARK 500 O HOH F 548 O HOH F 549 2.05 REMARK 500 O HOH F 540 O HOH F 558 2.09 REMARK 500 O HOH F 548 O HOH G 924 2.10 REMARK 500 O GLN F 128 N ILE F 130 2.11 REMARK 500 O LEU A 69 O HOH A 501 2.11 REMARK 500 NH1 ARG F 285 OP2 DT H 866 2.12 REMARK 500 O HOH F 507 O HOH F 582 2.12 REMARK 500 OP1 DA G 851 O HOH G 901 2.13 REMARK 500 OE1 GLU F 246 NZ LYS F 289 2.14 REMARK 500 NZ LYS F 191 O HOH F 402 2.15 REMARK 500 O HOH A 619 O HOH B 923 2.15 REMARK 500 O VAL A 303 O HOH A 502 2.16 REMARK 500 OG1 THR F 175 O HOH F 403 2.16 REMARK 500 O HOH A 629 O HOH A 639 2.16 REMARK 500 OD2 ASP A 108 O HOH A 503 2.16 REMARK 500 OE1 GLU A 301 O HOH A 504 2.17 REMARK 500 O HOH F 580 O HOH F 582 2.18 REMARK 500 NH1 ARG A 327 O HOH A 505 2.18 REMARK 500 OP2 DG C 861 O HOH C 901 2.19 REMARK 500 OE1 GLN F 227 O HOH F 404 2.19 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 NH1 ARG F 240 O5' DC C 857 2555 2.10 REMARK 500 O HOH A 609 O HOH A 613 2554 2.15 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 DT H 863 O3' DT H 863 C3' -0.044 REMARK 500 DG H 869 O3' DG H 869 C3' -0.039 REMARK 500 DA C 859 O3' DA C 859 C3' -0.036 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 DC G 838 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DG G 841 OP1 - P - OP2 ANGL. DEV. = 12.1 DEGREES REMARK 500 DG G 842 O5' - P - OP1 ANGL. DEV. = -6.3 DEGREES REMARK 500 DT G 844 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DA G 848 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DG B 850 C3' - C2' - C1' ANGL. DEV. = -5.7 DEGREES REMARK 500 DG B 850 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 DA C 859 O4' - C1' - N9 ANGL. DEV. = 2.4 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 THR F 94 148.76 -172.85 REMARK 500 ASP F 111 9.89 -69.96 REMARK 500 CYS F 115 48.34 -140.99 REMARK 500 GLN F 128 -145.77 -70.97 REMARK 500 THR F 129 -66.77 48.23 REMARK 500 SER F 236 -13.40 79.42 REMARK 500 LYS F 278 84.22 -159.36 REMARK 500 PHE F 295 -1.00 99.92 REMARK 500 TRP F 304 140.65 -173.13 REMARK 500 ALA A 56 -3.79 74.86 REMARK 500 ASP A 111 67.91 -115.81 REMARK 500 ASP A 230 96.64 -163.33 REMARK 500 ASN A 235 -66.24 -99.00 REMARK 500 SER A 236 -15.39 80.17 REMARK 500 LYS A 278 84.60 -164.19 REMARK 500 PHE A 295 -0.39 69.10 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 F 584 DISTANCE = 6.38 ANGSTROMS REMARK 525 HOH F 585 DISTANCE = 6.59 ANGSTROMS REMARK 525 HOH F 586 DISTANCE = 7.56 ANGSTROMS REMARK 525 HOH A 651 DISTANCE = 5.99 ANGSTROMS REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 8GT A 401 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 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 8 OD1 REMARK 620 2 MET A 9 O 85.7 REMARK 620 3 ASP A 103 OD2 115.8 93.9 REMARK 620 4 8GT A 401 O1G 83.4 88.5 160.8 REMARK 620 5 8GT A 401 O2B 165.0 87.5 78.0 83.1 REMARK 620 6 8GT A 401 O1A 100.8 173.2 85.1 90.3 85.7 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 8GT A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 402 DBREF 5C5J F 2 351 UNP W8STT9 W8STT9_ECOLX 2 351 DBREF 5C5J A 2 351 UNP W8STT9 W8STT9_ECOLX 2 351 DBREF 5C5J G 837 854 PDB 5C5J 5C5J 837 854 DBREF 5C5J H 856 873 PDB 5C5J 5C5J 856 873 DBREF 5C5J B 837 854 PDB 5C5J 5C5J 837 854 DBREF 5C5J C 856 873 PDB 5C5J 5C5J 856 873 SEQADV 5C5J GLY F 0 UNP W8STT9 EXPRESSION TAG SEQADV 5C5J SER F 1 UNP W8STT9 EXPRESSION TAG SEQADV 5C5J GLY A 0 UNP W8STT9 EXPRESSION TAG SEQADV 5C5J SER A 1 UNP W8STT9 EXPRESSION TAG SEQRES 1 F 352 GLY SER ARG LYS ILE ILE HIS VAL ASP MET ASP CYS PHE SEQRES 2 F 352 PHE ALA ALA VAL GLU MET ARG ASP ASN PRO ALA LEU ARG SEQRES 3 F 352 ASP ILE PRO ILE ALA ILE GLY GLY SER ARG GLU ARG ARG SEQRES 4 F 352 GLY VAL ILE SER THR ALA ASN TYR PRO ALA ARG LYS PHE SEQRES 5 F 352 GLY VAL ARG SER ALA MET PRO THR GLY MET ALA LEU LYS SEQRES 6 F 352 LEU CYS PRO HIS LEU THR LEU LEU PRO GLY ARG PHE ASP SEQRES 7 F 352 ALA TYR LYS GLU ALA SER ASN HIS ILE ARG GLU ILE PHE SEQRES 8 F 352 SER ARG TYR THR SER ARG ILE GLU PRO LEU SER LEU ASP SEQRES 9 F 352 GLU ALA TYR LEU ASP VAL THR ASP SER VAL HIS CYS HIS SEQRES 10 F 352 GLY SER ALA THR LEU ILE ALA GLN GLU ILE ARG GLN THR SEQRES 11 F 352 ILE PHE ASN GLU LEU GLN LEU THR ALA SER ALA GLY VAL SEQRES 12 F 352 ALA PRO VAL LYS PHE LEU ALA LYS ILE ALA SER ASP MET SEQRES 13 F 352 ASN LYS PRO ASN GLY GLN PHE VAL ILE THR PRO ALA GLU SEQRES 14 F 352 VAL PRO ALA PHE LEU GLN THR LEU PRO LEU ALA LYS ILE SEQRES 15 F 352 PRO GLY VAL GLY LYS VAL SER ALA ALA LYS LEU GLU ALA SEQRES 16 F 352 MET GLY LEU ARG THR CYS GLY ASP VAL GLN LYS CYS ASP SEQRES 17 F 352 LEU VAL MET LEU LEU LYS ARG PHE GLY LYS PHE GLY ARG SEQRES 18 F 352 ILE LEU TRP GLU ARG SER GLN GLY ILE ASP GLU ARG ASP SEQRES 19 F 352 VAL ASN SER GLU ARG LEU ARG LYS SER VAL GLY VAL GLU SEQRES 20 F 352 ARG THR MET ALA GLU ASP ILE HIS HIS TRP SER GLU CYS SEQRES 21 F 352 GLU ALA ILE ILE GLU ARG LEU TYR PRO GLU LEU GLU ARG SEQRES 22 F 352 ARG LEU ALA LYS VAL LYS PRO ASP LEU LEU ILE ALA ARG SEQRES 23 F 352 GLN GLY VAL LYS LEU LYS PHE ASP ASP PHE GLN GLN THR SEQRES 24 F 352 THR GLN GLU HIS VAL TRP PRO ARG LEU ASN LYS ALA ASP SEQRES 25 F 352 LEU ILE ALA THR ALA ARG LYS THR TRP ASP GLU ARG ARG SEQRES 26 F 352 GLY GLY ARG GLY VAL ARG LEU VAL GLY LEU HIS VAL THR SEQRES 27 F 352 LEU LEU ASP PRO GLN MET GLU ARG GLN LEU VAL LEU GLY SEQRES 28 F 352 LEU SEQRES 1 A 352 GLY SER ARG LYS ILE ILE HIS VAL ASP MET ASP CYS PHE SEQRES 2 A 352 PHE ALA ALA VAL GLU MET ARG ASP ASN PRO ALA LEU ARG SEQRES 3 A 352 ASP ILE PRO ILE ALA ILE GLY GLY SER ARG GLU ARG ARG SEQRES 4 A 352 GLY VAL ILE SER THR ALA ASN TYR PRO ALA ARG LYS PHE SEQRES 5 A 352 GLY VAL ARG SER ALA MET PRO THR GLY MET ALA LEU LYS SEQRES 6 A 352 LEU CYS PRO HIS LEU THR LEU LEU PRO GLY ARG PHE ASP SEQRES 7 A 352 ALA TYR LYS GLU ALA SER ASN HIS ILE ARG GLU ILE PHE SEQRES 8 A 352 SER ARG TYR THR SER ARG ILE GLU PRO LEU SER LEU ASP SEQRES 9 A 352 GLU ALA TYR LEU ASP VAL THR ASP SER VAL HIS CYS HIS SEQRES 10 A 352 GLY SER ALA THR LEU ILE ALA GLN GLU ILE ARG GLN THR SEQRES 11 A 352 ILE PHE ASN GLU LEU GLN LEU THR ALA SER ALA GLY VAL SEQRES 12 A 352 ALA PRO VAL LYS PHE LEU ALA LYS ILE ALA SER ASP MET SEQRES 13 A 352 ASN LYS PRO ASN GLY GLN PHE VAL ILE THR PRO ALA GLU SEQRES 14 A 352 VAL PRO ALA PHE LEU GLN THR LEU PRO LEU ALA LYS ILE SEQRES 15 A 352 PRO GLY VAL GLY LYS VAL SER ALA ALA LYS LEU GLU ALA SEQRES 16 A 352 MET GLY LEU ARG THR CYS GLY ASP VAL GLN LYS CYS ASP SEQRES 17 A 352 LEU VAL MET LEU LEU LYS ARG PHE GLY LYS PHE GLY ARG SEQRES 18 A 352 ILE LEU TRP GLU ARG SER GLN GLY ILE ASP GLU ARG ASP SEQRES 19 A 352 VAL ASN SER GLU ARG LEU ARG LYS SER VAL GLY VAL GLU SEQRES 20 A 352 ARG THR MET ALA GLU ASP ILE HIS HIS TRP SER GLU CYS SEQRES 21 A 352 GLU ALA ILE ILE GLU ARG LEU TYR PRO GLU LEU GLU ARG SEQRES 22 A 352 ARG LEU ALA LYS VAL LYS PRO ASP LEU LEU ILE ALA ARG SEQRES 23 A 352 GLN GLY VAL LYS LEU LYS PHE ASP ASP PHE GLN GLN THR SEQRES 24 A 352 THR GLN GLU HIS VAL TRP PRO ARG LEU ASN LYS ALA ASP SEQRES 25 A 352 LEU ILE ALA THR ALA ARG LYS THR TRP ASP GLU ARG ARG SEQRES 26 A 352 GLY GLY ARG GLY VAL ARG LEU VAL GLY LEU HIS VAL THR SEQRES 27 A 352 LEU LEU ASP PRO GLN MET GLU ARG GLN LEU VAL LEU GLY SEQRES 28 A 352 LEU SEQRES 1 G 18 DT DC DT DA DG DG DG DT DC DC DT DA DG SEQRES 2 G 18 DG DA DC DC DC SEQRES 1 H 18 DT DC DT DA DG DG DG DT DC DC DT DA DG SEQRES 2 H 18 DG DA DC DC DC SEQRES 1 B 18 DT DC DT DA DG DG DG DT DC DC DT DA DG SEQRES 2 B 18 DG DA DC DC DC SEQRES 1 C 18 DT DC DT DA DG DG DG DT DC DC DT DA DG SEQRES 2 C 18 DG DA DC DC DC HET 8GT A 401 32 HET MG A 402 1 HETNAM 8GT 8-OXO-GUANOSINE-5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 7 8GT C10 H16 N5 O15 P3 FORMUL 8 MG MG 2+ FORMUL 9 HOH *443(H2 O) HELIX 1 AA1 CYS F 11 ASN F 21 1 11 HELIX 2 AA2 PRO F 22 ARG F 25 5 4 HELIX 3 AA3 ASN F 45 PHE F 51 1 7 HELIX 4 AA4 PRO F 58 CYS F 66 1 9 HELIX 5 AA5 ARG F 75 ARG F 92 1 18 HELIX 6 AA6 SER F 118 GLN F 135 1 18 HELIX 7 AA7 VAL F 145 ASP F 154 1 10 HELIX 8 AA8 GLU F 168 THR F 175 1 8 HELIX 9 AA9 PRO F 177 ILE F 181 5 5 HELIX 10 AB1 GLY F 185 ALA F 194 1 10 HELIX 11 AB2 THR F 199 LYS F 205 1 7 HELIX 12 AB3 ASP F 207 GLY F 216 1 10 HELIX 13 AB4 GLY F 216 SER F 226 1 11 HELIX 14 AB5 HIS F 255 LYS F 278 1 24 HELIX 15 AB6 ASN F 308 ARG F 324 1 17 HELIX 16 AB7 CYS A 11 ASN A 21 1 11 HELIX 17 AB8 PRO A 22 ARG A 25 5 4 HELIX 18 AB9 ASN A 45 LYS A 50 1 6 HELIX 19 AC1 PRO A 58 CYS A 66 1 9 HELIX 20 AC2 ARG A 75 THR A 94 1 20 HELIX 21 AC3 SER A 118 GLN A 135 1 18 HELIX 22 AC4 VAL A 145 ASN A 156 1 12 HELIX 23 AC5 THR A 165 ALA A 167 5 3 HELIX 24 AC6 GLU A 168 THR A 175 1 8 HELIX 25 AC7 PRO A 177 ILE A 181 5 5 HELIX 26 AC8 GLY A 185 MET A 195 1 11 HELIX 27 AC9 THR A 199 LYS A 205 1 7 HELIX 28 AD1 ASP A 207 GLY A 216 1 10 HELIX 29 AD2 GLY A 216 SER A 226 1 11 HELIX 30 AD3 HIS A 255 LYS A 278 1 24 HELIX 31 AD4 ASN A 308 ARG A 324 1 17 SHEET 1 AA1 5 ILE F 97 SER F 101 0 SHEET 2 AA1 5 GLU F 104 ASP F 108 -1 O TYR F 106 N GLU F 98 SHEET 3 AA1 5 ILE F 4 MET F 9 -1 N ILE F 5 O LEU F 107 SHEET 4 AA1 5 ALA F 138 ALA F 143 -1 O SER F 139 N ASP F 8 SHEET 5 AA1 5 GLN F 161 VAL F 163 1 O PHE F 162 N VAL F 142 SHEET 1 AA2 3 ILE F 41 ALA F 44 0 SHEET 2 AA2 3 ILE F 29 GLY F 32 -1 N ILE F 31 O SER F 42 SHEET 3 AA2 3 THR F 70 LEU F 72 1 O LEU F 72 N GLY F 32 SHEET 1 AA3 4 SER F 242 ILE F 253 0 SHEET 2 AA3 4 VAL F 329 THR F 337 -1 O LEU F 334 N VAL F 245 SHEET 3 AA3 4 ARG F 285 PHE F 292 -1 N ARG F 285 O THR F 337 SHEET 4 AA3 4 GLN F 297 VAL F 303 -1 O GLN F 300 N VAL F 288 SHEET 1 AA4 5 ILE A 97 SER A 101 0 SHEET 2 AA4 5 GLU A 104 ASP A 108 -1 O GLU A 104 N LEU A 100 SHEET 3 AA4 5 ILE A 4 MET A 9 -1 N ILE A 5 O LEU A 107 SHEET 4 AA4 5 ALA A 138 ALA A 143 -1 O SER A 139 N ASP A 8 SHEET 5 AA4 5 GLN A 161 VAL A 163 1 O PHE A 162 N ALA A 140 SHEET 1 AA5 3 ILE A 41 ALA A 44 0 SHEET 2 AA5 3 ILE A 29 GLY A 32 -1 N ILE A 31 O SER A 42 SHEET 3 AA5 3 THR A 70 LEU A 72 1 O LEU A 72 N ALA A 30 SHEET 1 AA6 4 SER A 242 ILE A 253 0 SHEET 2 AA6 4 VAL A 329 THR A 337 -1 O LEU A 334 N VAL A 245 SHEET 3 AA6 4 ARG A 285 PHE A 292 -1 N ARG A 285 O THR A 337 SHEET 4 AA6 4 GLN A 297 VAL A 303 -1 O THR A 298 N LEU A 290 LINK OD1 ASP A 8 MG MG A 402 1555 1555 2.06 LINK O MET A 9 MG MG A 402 1555 1555 2.14 LINK OD2 ASP A 103 MG MG A 402 1555 1555 2.38 LINK O1G 8GT A 401 MG MG A 402 1555 1555 2.62 LINK O2B 8GT A 401 MG MG A 402 1555 1555 2.30 LINK O1A 8GT A 401 MG MG A 402 1555 1555 2.56 CISPEP 1 LYS F 157 PRO F 158 0 5.31 CISPEP 2 LYS A 157 PRO A 158 0 -1.16 SITE 1 AC1 19 ASP A 8 MET A 9 ASP A 10 CYS A 11 SITE 2 AC1 19 PHE A 12 PHE A 13 SER A 42 THR A 43 SITE 3 AC1 19 ARG A 49 SER A 55 ASP A 103 GLU A 104 SITE 4 AC1 19 LYS A 157 MG A 402 HOH A 507 HOH A 520 SITE 5 AC1 19 DA B 840 DG B 841 DC C 873 SITE 1 AC2 4 ASP A 8 MET A 9 ASP A 103 8GT A 401 CRYST1 86.450 57.380 110.640 90.00 94.51 90.00 P 1 21 1 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 0.011567 0.000000 0.000912 0.00000 SCALE2 0.000000 0.017428 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009066 0.00000