PDB Short entry for 4Q45 HEADER TRANSFERASE/DNA 13-APR-14 4Q45 TITLE DNA POLYMERASE- DAMAGED DNA COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE IV; COMPND 3 CHAIN: F, A; COMPND 4 FRAGMENT: UNP RESIDUES 2-341; COMPND 5 SYNONYM: POL IV; COMPND 6 EC: 2.7.7.7; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(*TP*CP*TP*AP*GP*GP*(RDG) COMPND 10 P*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3'); COMPND 11 CHAIN: G, B; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: DNA (5'- COMPND 15 D(*TP*CP*TP*A*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3'); COMPND 16 CHAIN: H, C; COMPND 17 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; 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: PGEX-6P1; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630; SOURCE 15 OTHER_DETAILS: CHEMICALLY SYNTHESIZED DNA; SOURCE 16 MOL_ID: 3; SOURCE 17 SYNTHETIC: YES; SOURCE 18 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 19 ORGANISM_TAXID: 32630; SOURCE 20 OTHER_DETAILS: CHEMICALLY SYNTHESIZED DNA KEYWDS POLYMERASE, DNA POLYMERASE, DNA, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.KOTTUR,A.SHARMA,D.T.NAIR REVDAT 2 20-MAR-24 4Q45 1 REMARK SEQADV LINK REVDAT 1 06-MAY-15 4Q45 0 JRNL AUTH J.KOTTUR,A.SHARMA,K.R.GORE,N.NARAYANAN,B.SAMANTA, JRNL AUTH 2 P.I.PRADEEPKUMAR,D.T.NAIR JRNL TITL UNIQUE STRUCTURAL FEATURES IN DNA POLYMERASE IV ENABLE JRNL TITL 2 EFFICIENT BYPASS OF THE N2 ADDUCT INDUCED BY THE JRNL TITL 3 NITROFURAZONE ANTIBIOTIC JRNL REF STRUCTURE V. 23 56 2015 JRNL REFN ISSN 0969-2126 JRNL PMID 25497730 JRNL DOI 10.1016/J.STR.2014.10.019 REMARK 2 REMARK 2 RESOLUTION. 2.18 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8_1069) 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) : 2.18 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 51.34 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.910 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.0 REMARK 3 NUMBER OF REFLECTIONS : 100631 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.214 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 5101 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 51.3536 - 6.7564 0.90 3209 169 0.1561 0.2098 REMARK 3 2 6.7564 - 5.3646 0.91 3197 161 0.1891 0.1967 REMARK 3 3 5.3646 - 4.6870 0.96 3389 205 0.1697 0.2208 REMARK 3 4 4.6870 - 4.2587 0.96 3425 183 0.1585 0.1651 REMARK 3 5 4.2587 - 3.9536 0.95 3348 187 0.1703 0.2361 REMARK 3 6 3.9536 - 3.7206 0.86 3029 150 0.1837 0.2380 REMARK 3 7 3.7206 - 3.5343 0.81 2891 146 0.1889 0.2182 REMARK 3 8 3.5343 - 3.3805 0.87 3068 154 0.1870 0.2311 REMARK 3 9 3.3805 - 3.2503 0.90 3164 190 0.1920 0.2494 REMARK 3 10 3.2503 - 3.1382 0.92 3273 158 0.2128 0.2333 REMARK 3 11 3.1382 - 3.0401 0.94 3283 168 0.2170 0.2913 REMARK 3 12 3.0401 - 2.9532 0.96 3437 174 0.2221 0.2501 REMARK 3 13 2.9532 - 2.8755 0.96 3370 178 0.2334 0.2821 REMARK 3 14 2.8755 - 2.8053 0.95 3420 187 0.2371 0.2833 REMARK 3 15 2.8053 - 2.7415 0.95 3356 193 0.2386 0.2882 REMARK 3 16 2.7415 - 2.6832 0.92 3239 174 0.2340 0.2913 REMARK 3 17 2.6832 - 2.6295 0.89 3119 173 0.2516 0.2906 REMARK 3 18 2.6295 - 2.5799 0.85 3028 148 0.2493 0.2944 REMARK 3 19 2.5799 - 2.5338 0.83 2937 151 0.2568 0.2955 REMARK 3 20 2.5338 - 2.4909 0.78 2748 151 0.3155 0.4025 REMARK 3 21 2.4909 - 2.4507 0.87 3088 150 0.2600 0.2724 REMARK 3 22 2.4507 - 2.4130 0.90 3164 175 0.2438 0.3178 REMARK 3 23 2.4130 - 2.3775 0.91 3239 191 0.2623 0.3178 REMARK 3 24 2.3775 - 2.3440 0.90 3145 194 0.2533 0.3095 REMARK 3 25 2.3440 - 2.3123 0.89 3094 172 0.2648 0.3207 REMARK 3 26 2.3123 - 2.2823 0.86 3112 150 0.3898 0.4656 REMARK 3 27 2.2823 - 2.2538 0.87 3076 144 0.3750 0.4529 REMARK 3 28 2.2538 - 2.2266 0.88 3088 180 0.4035 0.4273 REMARK 3 29 2.2266 - 2.2007 0.92 3206 183 0.3365 0.3952 REMARK 3 30 2.2007 - 2.1760 0.93 3388 162 0.2962 0.3512 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) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.180 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.14 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 : 0.005 7069 REMARK 3 ANGLE : 1.051 9847 REMARK 3 CHIRALITY : 0.065 1106 REMARK 3 PLANARITY : 0.004 1035 REMARK 3 DIHEDRAL : 20.347 2770 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: THE ENTRY CONTAINS FRIEDEL PAIRS IN REMARK 3 F_PLUS/MINUS COLUMNS REMARK 4 REMARK 4 4Q45 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-APR-14. REMARK 100 THE DEPOSITION ID IS D_1000085580. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-AUG-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 100631 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.176 REMARK 200 RESOLUTION RANGE LOW (A) : 51.340 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.18 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.29 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.32800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.900 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: NULL REMARK 200 REMARK 200 REMARK: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.78 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M ACETATE, PH 4.8, VAPOR DIFFUSION, REMARK 280 HANGING 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 28.95000 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: 4800 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20550 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -49.0 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: 4830 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21470 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -47.0 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 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 DG H 860 P OP1 OP2 REMARK 470 DC C 857 P OP1 OP2 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 O2 DT H 866 O HOH H 927 1.81 REMARK 500 O HOH F 669 O HOH F 678 1.92 REMARK 500 O HOH F 571 O HOH F 574 1.96 REMARK 500 O HOH F 573 O HOH G 924 1.97 REMARK 500 O HOH H 902 O HOH H 925 2.00 REMARK 500 OP1 DG C 861 O HOH C 931 2.01 REMARK 500 O HOH A 590 O HOH B 926 2.01 REMARK 500 O ALA A 250 O HOH A 590 2.02 REMARK 500 O HOH H 905 O HOH H 911 2.02 REMARK 500 O HOH B 904 O HOH B 922 2.04 REMARK 500 OE2 GLU F 246 O HOH F 504 2.04 REMARK 500 NH1 ARG A 37 O HOH A 570 2.05 REMARK 500 O4 DT H 866 O HOH H 923 2.07 REMARK 500 NH2 ARG F 317 O HOH F 634 2.08 REMARK 500 O HOH A 589 O HOH B 901 2.09 REMARK 500 O HOH A 585 O HOH B 913 2.09 REMARK 500 O VAL F 113 O HOH F 641 2.11 REMARK 500 O HOH C 923 O HOH C 927 2.14 REMARK 500 O HOH A 589 O HOH B 908 2.14 REMARK 500 O ASP F 293 O HOH F 594 2.14 REMARK 500 NE2 GLN A 174 O HOH A 584 2.14 REMARK 500 OE1 GLN F 297 O HOH F 631 2.15 REMARK 500 O HOH A 589 O HOH A 597 2.15 REMARK 500 N2 DG H 862 O HOH H 928 2.17 REMARK 500 NE ARG F 127 O HOH F 659 2.19 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 G 842 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DA G 848 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 DC G 852 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DC G 853 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DG H 860 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DC B 838 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 DT B 839 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DG B 841 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DA C 859 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DG C 861 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DG C 868 O4' - C1' - N9 ANGL. DEV. = 4.4 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 CYS F 11 48.26 39.97 REMARK 500 SER F 101 178.30 176.72 REMARK 500 THR F 129 -18.90 50.50 REMARK 500 GLU F 133 -47.91 65.52 REMARK 500 MET F 195 34.61 -85.64 REMARK 500 ASP F 230 92.19 -160.80 REMARK 500 ASN F 235 -73.73 -75.13 REMARK 500 SER F 236 -14.53 85.10 REMARK 500 ALA A 56 -3.04 72.37 REMARK 500 SER A 101 -168.92 -166.55 REMARK 500 HIS A 114 -92.27 -65.39 REMARK 500 THR A 129 -57.02 99.80 REMARK 500 GLU A 133 -57.15 55.26 REMARK 500 ASN A 156 42.34 -107.21 REMARK 500 ASP A 230 85.24 -158.53 REMARK 500 ASN A 235 -96.99 -74.74 REMARK 500 SER A 236 -15.82 100.25 REMARK 500 PHE A 295 -6.44 74.66 REMARK 500 ASP A 340 -76.59 -64.88 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 MG F 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP F 8 OD1 REMARK 620 2 MET F 9 O 85.5 REMARK 620 3 ASP F 103 OD1 90.2 89.5 REMARK 620 4 1FZ F 401 O2A 107.7 166.5 93.6 REMARK 620 5 1FZ F 401 O1B 174.6 93.2 95.0 73.4 REMARK 620 6 1FZ F 401 O1G 101.1 92.7 168.6 81.8 73.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG F 403 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP F 103 OD2 REMARK 620 2 ASP F 103 OD1 50.2 REMARK 620 3 GLU F 104 OE1 138.3 151.4 REMARK 620 4 1FZ F 401 O2A 115.8 72.5 105.7 REMARK 620 5 DC H 873 O3' 70.3 106.7 101.0 107.7 REMARK 620 N 1 2 3 4 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 85.5 REMARK 620 3 ASP A 103 OD2 88.8 91.3 REMARK 620 4 1FZ A 401 O1A 99.1 175.1 90.6 REMARK 620 5 1FZ A 401 O1G 101.1 89.9 170.1 87.5 REMARK 620 6 1FZ A 401 O2B 176.7 97.4 89.5 78.0 80.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 403 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 8 OD2 REMARK 620 2 GLU A 104 OE2 74.8 REMARK 620 3 1FZ A 401 O1A 94.2 105.6 REMARK 620 4 1FZ A 401 O2A 150.2 113.8 56.2 REMARK 620 5 HOH A 586 O 69.8 140.7 93.7 105.4 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 1FZ F 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG F 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG F 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 1FZ A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 403 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4Q43 RELATED DB: PDB REMARK 900 RELATED ID: 4Q44 RELATED DB: PDB DBREF 4Q45 F 2 341 UNP Q47155 DPO4_ECOLI 2 341 DBREF 4Q45 A 2 341 UNP Q47155 DPO4_ECOLI 2 341 DBREF 4Q45 G 837 854 PDB 4Q45 4Q45 837 854 DBREF 4Q45 B 837 854 PDB 4Q45 4Q45 837 854 DBREF 4Q45 H 856 873 PDB 4Q45 4Q45 856 873 DBREF 4Q45 C 856 873 PDB 4Q45 4Q45 856 873 SEQADV 4Q45 GLY F 0 UNP Q47155 EXPRESSION TAG SEQADV 4Q45 SER F 1 UNP Q47155 EXPRESSION TAG SEQADV 4Q45 ALA F 64 UNP Q47155 LYS 64 CONFLICT SEQADV 4Q45 ALA F 205 UNP Q47155 LYS 205 CONFLICT SEQADV 4Q45 GLY A 0 UNP Q47155 EXPRESSION TAG SEQADV 4Q45 SER A 1 UNP Q47155 EXPRESSION TAG SEQADV 4Q45 ALA A 64 UNP Q47155 LYS 64 CONFLICT SEQADV 4Q45 ALA A 205 UNP Q47155 LYS 205 CONFLICT SEQRES 1 F 342 GLY SER ARG LYS ILE ILE HIS VAL ASP MET ASP CYS PHE SEQRES 2 F 342 PHE ALA ALA VAL GLU MET ARG ASP ASN PRO ALA LEU ARG SEQRES 3 F 342 ASP ILE PRO ILE ALA ILE GLY GLY SER ARG GLU ARG ARG SEQRES 4 F 342 GLY VAL ILE SER THR ALA ASN TYR PRO ALA ARG LYS PHE SEQRES 5 F 342 GLY VAL ARG SER ALA MET PRO THR GLY MET ALA LEU ALA SEQRES 6 F 342 LEU CYS PRO HIS LEU THR LEU LEU PRO GLY ARG PHE ASP SEQRES 7 F 342 ALA TYR LYS GLU ALA SER ASN HIS ILE ARG GLU ILE PHE SEQRES 8 F 342 SER ARG TYR THR SER ARG ILE GLU PRO LEU SER LEU ASP SEQRES 9 F 342 GLU ALA TYR LEU ASP VAL THR ASP SER VAL HIS CYS HIS SEQRES 10 F 342 GLY SER ALA THR LEU ILE ALA GLN GLU ILE ARG GLN THR SEQRES 11 F 342 ILE PHE ASN GLU LEU GLN LEU THR ALA SER ALA GLY VAL SEQRES 12 F 342 ALA PRO VAL LYS PHE LEU ALA LYS ILE ALA SER ASP MET SEQRES 13 F 342 ASN LYS PRO ASN GLY GLN PHE VAL ILE THR PRO ALA GLU SEQRES 14 F 342 VAL PRO ALA PHE LEU GLN THR LEU PRO LEU ALA LYS ILE SEQRES 15 F 342 PRO GLY VAL GLY LYS VAL SER ALA ALA LYS LEU GLU ALA SEQRES 16 F 342 MET GLY LEU ARG THR CYS GLY ASP VAL GLN ALA CYS ASP SEQRES 17 F 342 LEU VAL MET LEU LEU LYS ARG PHE GLY LYS PHE GLY ARG SEQRES 18 F 342 ILE LEU TRP GLU ARG SER GLN GLY ILE ASP GLU ARG ASP SEQRES 19 F 342 VAL ASN SER GLU ARG LEU ARG LYS SER VAL GLY VAL GLU SEQRES 20 F 342 ARG THR MET ALA GLU ASP ILE HIS HIS TRP SER GLU CYS SEQRES 21 F 342 GLU ALA ILE ILE GLU ARG LEU TYR PRO GLU LEU GLU ARG SEQRES 22 F 342 ARG LEU ALA LYS VAL LYS PRO ASP LEU LEU ILE ALA ARG SEQRES 23 F 342 GLN GLY VAL LYS LEU LYS PHE ASP ASP PHE GLN GLN THR SEQRES 24 F 342 THR GLN GLU HIS VAL TRP PRO ARG LEU ASN LYS ALA ASP SEQRES 25 F 342 LEU ILE ALA THR ALA ARG LYS THR TRP ASP GLU ARG ARG SEQRES 26 F 342 GLY GLY ARG GLY VAL ARG LEU VAL GLY LEU HIS VAL THR SEQRES 27 F 342 LEU LEU ASP PRO SEQRES 1 A 342 GLY SER ARG LYS ILE ILE HIS VAL ASP MET ASP CYS PHE SEQRES 2 A 342 PHE ALA ALA VAL GLU MET ARG ASP ASN PRO ALA LEU ARG SEQRES 3 A 342 ASP ILE PRO ILE ALA ILE GLY GLY SER ARG GLU ARG ARG SEQRES 4 A 342 GLY VAL ILE SER THR ALA ASN TYR PRO ALA ARG LYS PHE SEQRES 5 A 342 GLY VAL ARG SER ALA MET PRO THR GLY MET ALA LEU ALA SEQRES 6 A 342 LEU CYS PRO HIS LEU THR LEU LEU PRO GLY ARG PHE ASP SEQRES 7 A 342 ALA TYR LYS GLU ALA SER ASN HIS ILE ARG GLU ILE PHE SEQRES 8 A 342 SER ARG TYR THR SER ARG ILE GLU PRO LEU SER LEU ASP SEQRES 9 A 342 GLU ALA TYR LEU ASP VAL THR ASP SER VAL HIS CYS HIS SEQRES 10 A 342 GLY SER ALA THR LEU ILE ALA GLN GLU ILE ARG GLN THR SEQRES 11 A 342 ILE PHE ASN GLU LEU GLN LEU THR ALA SER ALA GLY VAL SEQRES 12 A 342 ALA PRO VAL LYS PHE LEU ALA LYS ILE ALA SER ASP MET SEQRES 13 A 342 ASN LYS PRO ASN GLY GLN PHE VAL ILE THR PRO ALA GLU SEQRES 14 A 342 VAL PRO ALA PHE LEU GLN THR LEU PRO LEU ALA LYS ILE SEQRES 15 A 342 PRO GLY VAL GLY LYS VAL SER ALA ALA LYS LEU GLU ALA SEQRES 16 A 342 MET GLY LEU ARG THR CYS GLY ASP VAL GLN ALA CYS ASP SEQRES 17 A 342 LEU VAL MET LEU LEU LYS ARG PHE GLY LYS PHE GLY ARG SEQRES 18 A 342 ILE LEU TRP GLU ARG SER GLN GLY ILE ASP GLU ARG ASP SEQRES 19 A 342 VAL ASN SER GLU ARG LEU ARG LYS SER VAL GLY VAL GLU SEQRES 20 A 342 ARG THR MET ALA GLU ASP ILE HIS HIS TRP SER GLU CYS SEQRES 21 A 342 GLU ALA ILE ILE GLU ARG LEU TYR PRO GLU LEU GLU ARG SEQRES 22 A 342 ARG LEU ALA LYS VAL LYS PRO ASP LEU LEU ILE ALA ARG SEQRES 23 A 342 GLN GLY VAL LYS LEU LYS PHE ASP ASP PHE GLN GLN THR SEQRES 24 A 342 THR GLN GLU HIS VAL TRP PRO ARG LEU ASN LYS ALA ASP SEQRES 25 A 342 LEU ILE ALA THR ALA ARG LYS THR TRP ASP GLU ARG ARG SEQRES 26 A 342 GLY GLY ARG GLY VAL ARG LEU VAL GLY LEU HIS VAL THR SEQRES 27 A 342 LEU LEU ASP PRO SEQRES 1 G 18 DT DC DT DA DG DG RDG 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 RDG 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 MODRES 4Q45 RDG G 843 DG MODRES 4Q45 RDG B 843 DG HET RDG G 843 28 HET RDG B 843 28 HET 1FZ F 401 29 HET MG F 402 1 HET MG F 403 1 HET 1FZ A 401 29 HET MG A 402 1 HET MG A 403 1 HETNAM RDG 2'-DEOXY-N-(FURAN-2-YLMETHYL)GUANOSINE 5'-(DIHYDROGEN HETNAM 2 RDG PHOSPHATE) HETNAM 1FZ 5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY) HETNAM 2 1FZ PHOSPHORYL]AMINO}PHOSPHORYL]THYMIDINE HETNAM MG MAGNESIUM ION HETSYN RDG N2-FURFURYL-DEOXYGUANOSINE-5'-MONOPHOSPHATE FORMUL 3 RDG 2(C15 H18 N5 O8 P) FORMUL 7 1FZ 2(C10 H18 N3 O13 P3) FORMUL 8 MG 4(MG 2+) FORMUL 13 HOH *424(H2 O) HELIX 1 1 CYS F 11 ASN F 21 1 11 HELIX 2 2 PRO F 22 ARG F 25 5 4 HELIX 3 3 SER F 34 ARG F 38 5 5 HELIX 4 4 ASN F 45 LYS F 50 1 6 HELIX 5 5 PRO F 58 CYS F 66 1 9 HELIX 6 6 ARG F 75 ARG F 92 1 18 HELIX 7 7 VAL F 113 GLY F 117 5 5 HELIX 8 8 SER F 118 GLN F 128 1 11 HELIX 9 9 ILE F 130 GLN F 135 1 6 HELIX 10 10 VAL F 145 ASN F 156 1 12 HELIX 11 11 THR F 165 ALA F 167 5 3 HELIX 12 12 GLU F 168 LEU F 176 1 9 HELIX 13 13 PRO F 177 ILE F 181 5 5 HELIX 14 14 GLY F 185 MET F 195 1 11 HELIX 15 15 THR F 199 ALA F 205 1 7 HELIX 16 16 ASP F 207 GLY F 216 1 10 HELIX 17 17 GLY F 216 GLN F 227 1 12 HELIX 18 18 HIS F 255 LYS F 278 1 24 HELIX 19 19 ASN F 308 ARG F 324 1 17 HELIX 20 20 CYS A 11 ASN A 21 1 11 HELIX 21 21 PRO A 22 ARG A 25 5 4 HELIX 22 22 ASN A 45 LYS A 50 1 6 HELIX 23 23 PRO A 58 CYS A 66 1 9 HELIX 24 24 ARG A 75 ARG A 92 1 18 HELIX 25 25 SER A 118 GLN A 135 1 18 HELIX 26 26 VAL A 145 ASN A 156 1 12 HELIX 27 27 GLU A 168 THR A 175 1 8 HELIX 28 28 PRO A 177 ILE A 181 5 5 HELIX 29 29 GLY A 185 MET A 195 1 11 HELIX 30 30 THR A 199 ALA A 205 1 7 HELIX 31 31 ASP A 207 GLN A 227 1 21 HELIX 32 32 HIS A 255 LYS A 276 1 22 HELIX 33 33 ASN A 308 ARG A 324 1 17 SHEET 1 A 5 ILE F 97 SER F 101 0 SHEET 2 A 5 GLU F 104 ASP F 108 -1 O TYR F 106 N GLU F 98 SHEET 3 A 5 ILE F 4 MET F 9 -1 N ILE F 5 O LEU F 107 SHEET 4 A 5 ALA F 138 ALA F 143 -1 O SER F 139 N ASP F 8 SHEET 5 A 5 GLN F 161 VAL F 163 1 O PHE F 162 N VAL F 142 SHEET 1 B 3 ILE F 41 ALA F 44 0 SHEET 2 B 3 ILE F 29 GLY F 32 -1 N ILE F 31 O SER F 42 SHEET 3 B 3 THR F 70 LEU F 72 1 O LEU F 72 N ALA F 30 SHEET 1 C 4 SER F 242 ILE F 253 0 SHEET 2 C 4 VAL F 329 THR F 337 -1 O LEU F 334 N VAL F 245 SHEET 3 C 4 ARG F 285 PHE F 292 -1 N LYS F 289 O GLY F 333 SHEET 4 C 4 GLN F 297 VAL F 303 -1 O THR F 298 N LEU F 290 SHEET 1 D 5 ILE A 97 PRO A 99 0 SHEET 2 D 5 GLU A 104 ASP A 108 -1 O TYR A 106 N GLU A 98 SHEET 3 D 5 ILE A 4 MET A 9 -1 N VAL A 7 O ALA A 105 SHEET 4 D 5 ALA A 138 ALA A 143 -1 O ALA A 143 N ILE A 4 SHEET 5 D 5 GLN A 161 VAL A 163 1 O PHE A 162 N VAL A 142 SHEET 1 E 3 ILE A 41 ALA A 44 0 SHEET 2 E 3 ILE A 29 GLY A 32 -1 N ILE A 31 O SER A 42 SHEET 3 E 3 THR A 70 LEU A 72 1 O LEU A 72 N ALA A 30 SHEET 1 F 4 SER A 242 ILE A 253 0 SHEET 2 F 4 VAL A 329 THR A 337 -1 O LEU A 334 N VAL A 245 SHEET 3 F 4 ARG A 285 PHE A 292 -1 N ARG A 285 O THR A 337 SHEET 4 F 4 GLN A 297 VAL A 303 -1 O THR A 298 N LEU A 290 LINK O3' DG G 842 P RDG G 843 1555 1555 1.61 LINK O3' RDG G 843 P DT G 844 1555 1555 1.61 LINK O3' DG B 842 P RDG B 843 1555 1555 1.61 LINK O3' RDG B 843 P DT B 844 1555 1555 1.61 LINK OD1 ASP F 8 MG MG F 402 1555 1555 1.96 LINK O MET F 9 MG MG F 402 1555 1555 2.31 LINK OD1 ASP F 103 MG MG F 402 1555 1555 2.34 LINK OD2 ASP F 103 MG MG F 403 1555 1555 2.15 LINK OD1 ASP F 103 MG MG F 403 1555 1555 2.81 LINK OE1 GLU F 104 MG MG F 403 1555 1555 2.17 LINK O2A 1FZ F 401 MG MG F 402 1555 1555 2.05 LINK O1B 1FZ F 401 MG MG F 402 1555 1555 2.12 LINK O1G 1FZ F 401 MG MG F 402 1555 1555 2.31 LINK O2A 1FZ F 401 MG MG F 403 1555 1555 2.61 LINK MG MG F 403 O3' DC H 873 1555 1555 2.83 LINK OD1 ASP A 8 MG MG A 402 1555 1555 2.05 LINK OD2 ASP A 8 MG MG A 403 1555 1555 2.65 LINK O MET A 9 MG MG A 402 1555 1555 2.26 LINK OD2 ASP A 103 MG MG A 402 1555 1555 2.36 LINK OE2 GLU A 104 MG MG A 403 1555 1555 2.24 LINK O1A 1FZ A 401 MG MG A 402 1555 1555 2.04 LINK O1G 1FZ A 401 MG MG A 402 1555 1555 2.14 LINK O2B 1FZ A 401 MG MG A 402 1555 1555 2.15 LINK O1A 1FZ A 401 MG MG A 403 1555 1555 2.52 LINK O2A 1FZ A 401 MG MG A 403 1555 1555 2.75 LINK MG MG A 403 O HOH A 586 1555 1555 2.83 CISPEP 1 LYS F 157 PRO F 158 0 2.09 CISPEP 2 LYS A 157 PRO A 158 0 -0.94 SITE 1 AC1 23 ASP F 8 MET F 9 ASP F 10 CYS F 11 SITE 2 AC1 23 PHE F 12 PHE F 13 SER F 42 THR F 43 SITE 3 AC1 23 ARG F 49 ASP F 103 LYS F 157 MG F 402 SITE 4 AC1 23 MG F 403 HOH F 507 HOH F 508 HOH F 525 SITE 5 AC1 23 HOH F 528 HOH F 583 HOH F 635 HOH F 673 SITE 6 AC1 23 HOH F 674 DA G 840 DC H 873 SITE 1 AC2 5 ASP F 8 MET F 9 ASP F 103 1FZ F 401 SITE 2 AC2 5 MG F 403 SITE 1 AC3 7 ASP F 8 ASP F 103 GLU F 104 1FZ F 401 SITE 2 AC3 7 MG F 402 HOH F 673 DC H 873 SITE 1 AC4 19 ASP A 8 MET A 9 ASP A 10 CYS A 11 SITE 2 AC4 19 PHE A 12 PHE A 13 SER A 42 THR A 43 SITE 3 AC4 19 ARG A 49 SER A 55 ASP A 103 LYS A 157 SITE 4 AC4 19 MG A 402 MG A 403 HOH A 522 HOH A 523 SITE 5 AC4 19 HOH A 543 DA B 840 DC C 873 SITE 1 AC5 5 ASP A 8 MET A 9 ASP A 103 LYS A 157 SITE 2 AC5 5 1FZ A 401 SITE 1 AC6 4 ASP A 8 GLU A 104 1FZ A 401 HOH A 586 CRYST1 85.500 57.900 111.040 90.00 90.44 90.00 P 1 21 1 4 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 0.011696 0.000000 0.000090 0.00000 SCALE2 0.000000 0.017271 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009006 0.00000