PDB Short entry for 4Q44 HEADER TRANSFERASE/DNA 13-APR-14 4Q44 TITLE POLYMERASE-DAMAGED DNA COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE IV; COMPND 3 CHAIN: A, F; 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*(RDG) COMPND 10 P*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3'); COMPND 11 CHAIN: B, C, G, H; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: B0231; 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: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630; SOURCE 15 OTHER_DETAILS: CHEMICALLY SYNTHESIZED DNA OLIGONUCLEOTIDE KEYWDS POLYMERASE, DNA POLYMERASE, DNA, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR D.T.NAIR,J.KOTTUR,A.SHARMA REVDAT 2 08-NOV-23 4Q44 1 REMARK SEQADV LINK REVDAT 1 06-MAY-15 4Q44 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. 2.71 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) : 2.71 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.21 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 29593 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.227 REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 1501 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 48.2171 - 6.0127 0.99 2639 162 0.1756 0.2127 REMARK 3 2 6.0127 - 4.7739 1.00 2569 143 0.2100 0.2158 REMARK 3 3 4.7739 - 4.1708 1.00 2586 138 0.1888 0.2256 REMARK 3 4 4.1708 - 3.7896 1.00 2572 125 0.2078 0.2435 REMARK 3 5 3.7896 - 3.5181 1.00 2567 150 0.2253 0.2995 REMARK 3 6 3.5181 - 3.3107 1.00 2545 120 0.2412 0.3178 REMARK 3 7 3.3107 - 3.1450 1.00 2525 143 0.2616 0.3335 REMARK 3 8 3.1450 - 3.0081 1.00 2533 151 0.2812 0.3349 REMARK 3 9 3.0081 - 2.8923 1.00 2529 131 0.2967 0.3551 REMARK 3 10 2.8923 - 2.7925 0.99 2538 138 0.3114 0.3880 REMARK 3 11 2.7925 - 2.7052 0.98 2489 100 0.3156 0.3336 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) : 29.780 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 62.40 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 : 0.003 7082 REMARK 3 ANGLE : 0.845 9865 REMARK 3 CHIRALITY : 0.057 1103 REMARK 3 PLANARITY : 0.004 1037 REMARK 3 DIHEDRAL : 21.015 2759 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 4Q44 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-APR-14. REMARK 100 THE DEPOSITION ID IS D_1000085579. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-MAY-12 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 : 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) : 1.0 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29593 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.75 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.51600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.200 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: 4IR1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.74 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 28.46700 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: 4880 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -48.0 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 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: 4850 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20440 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -50.0 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 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 C 856 REMARK 465 DT H 856 REMARK 465 DC H 857 REMARK 465 DT H 858 REMARK 465 DA H 859 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 A 3 CG CD CE NZ 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 O ASN F 235 O HOH F 520 1.81 REMARK 500 O4 DT H 863 O HOH H 907 1.83 REMARK 500 O1G 1FZ F 401 O HOH F 524 1.90 REMARK 500 OD2 ASP A 154 O HOH A 504 1.98 REMARK 500 O6 DG G 849 O HOH G 903 2.05 REMARK 500 O ASP F 230 O HOH F 501 2.07 REMARK 500 O HOH A 502 O HOH C 901 2.09 REMARK 500 N ASP F 311 O HOH F 521 2.15 REMARK 500 OD2 ASP F 8 O HOH F 522 2.15 REMARK 500 O2A 1FZ A 401 O HOH A 507 2.16 REMARK 500 OE2 GLU F 301 O HOH F 523 2.16 REMARK 500 N GLY F 117 O HOH F 504 2.18 REMARK 500 O VAL F 184 O HOH F 506 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 DA B 848 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 DG B 850 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DC C 857 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DT C 858 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DA G 848 O4' - C1' - N9 ANGL. DEV. = 2.3 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 ASN A 21 82.38 -155.54 REMARK 500 LEU A 24 -111.07 -77.64 REMARK 500 ARG A 25 -60.37 55.91 REMARK 500 ARG A 96 90.63 -69.79 REMARK 500 SER A 101 -145.24 -160.95 REMARK 500 ASP A 111 0.49 -69.10 REMARK 500 CYS A 115 58.92 -118.16 REMARK 500 THR A 175 31.78 -98.00 REMARK 500 ALA A 205 33.16 -99.63 REMARK 500 SER A 236 -4.87 70.17 REMARK 500 GLU A 251 -110.90 145.84 REMARK 500 ASP A 252 -115.96 43.30 REMARK 500 ILE A 253 90.27 39.97 REMARK 500 LYS A 278 96.66 -167.48 REMARK 500 LEU A 281 80.44 59.84 REMARK 500 LEU A 282 -102.07 -62.63 REMARK 500 ILE A 283 117.67 88.16 REMARK 500 LEU A 338 174.83 63.54 REMARK 500 CYS F 11 52.35 34.38 REMARK 500 SER F 101 -164.88 -168.30 REMARK 500 ASP F 111 39.57 -96.00 REMARK 500 VAL F 113 -10.37 -146.33 REMARK 500 HIS F 114 -72.82 -62.90 REMARK 500 CYS F 115 49.16 -94.80 REMARK 500 THR F 129 -29.05 89.03 REMARK 500 GLU F 133 -54.73 62.87 REMARK 500 ARG F 198 -38.96 -131.53 REMARK 500 SER F 236 -7.13 67.85 REMARK 500 TRP F 304 129.75 -174.10 REMARK 500 LEU F 307 104.21 -45.49 REMARK 500 ARG F 323 91.07 -164.57 REMARK 500 ARG F 324 -20.24 -168.65 REMARK 500 ASP F 340 -120.58 -73.93 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ASP F 340 PRO F 341 -145.72 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 A 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 8 OD1 REMARK 620 2 MET A 9 O 86.3 REMARK 620 3 ASP A 103 OD2 103.4 92.0 REMARK 620 4 1FZ A 401 O2B 151.8 84.0 103.3 REMARK 620 5 1FZ A 401 O1A 108.2 164.6 89.7 80.7 REMARK 620 6 1FZ A 401 O1G 83.4 87.0 173.0 69.7 89.5 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 86.5 REMARK 620 3 1FZ A 401 O1A 108.8 104.2 REMARK 620 4 HOH A 502 O 95.0 157.8 96.3 REMARK 620 5 HOH C 901 O 119.3 113.5 119.0 47.1 REMARK 620 N 1 2 3 4 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 95.6 REMARK 620 3 ASP F 103 OD2 87.0 124.3 REMARK 620 4 1FZ F 401 O2B 143.4 99.5 110.7 REMARK 620 5 1FZ F 401 O2A 88.2 162.5 72.8 68.4 REMARK 620 N 1 2 3 4 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 OD1 REMARK 620 2 ASP F 103 OD2 54.5 REMARK 620 3 GLU F 104 OE2 147.0 150.2 REMARK 620 4 1FZ F 401 O2A 116.9 71.9 95.9 REMARK 620 5 DC H 873 O3' 69.8 110.0 99.3 105.0 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 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 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 1FZ F 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG F 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG F 403 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4Q43 RELATED DB: PDB REMARK 900 RELATED ID: 4Q45 RELATED DB: PDB DBREF 4Q44 A 2 341 UNP Q47155 DPO4_ECOLI 2 341 DBREF 4Q44 F 2 341 UNP Q47155 DPO4_ECOLI 2 341 DBREF 4Q44 B 837 854 PDB 4Q44 4Q44 837 854 DBREF 4Q44 C 856 873 PDB 4Q44 4Q44 856 873 DBREF 4Q44 G 837 854 PDB 4Q44 4Q44 837 854 DBREF 4Q44 H 856 873 PDB 4Q44 4Q44 856 873 SEQADV 4Q44 GLY A 0 UNP Q47155 EXPRESSION TAG SEQADV 4Q44 SER A 1 UNP Q47155 EXPRESSION TAG SEQADV 4Q44 ALA A 64 UNP Q47155 LYS 64 CONFLICT SEQADV 4Q44 ALA A 205 UNP Q47155 LYS 205 CONFLICT SEQADV 4Q44 GLY F 0 UNP Q47155 EXPRESSION TAG SEQADV 4Q44 SER F 1 UNP Q47155 EXPRESSION TAG SEQADV 4Q44 ALA F 64 UNP Q47155 LYS 64 CONFLICT SEQADV 4Q44 ALA F 205 UNP Q47155 LYS 205 CONFLICT 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 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 B 18 DT DC DT DA RDG 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 RDG DG DG DT DC DC DT DA DG SEQRES 2 C 18 DG DA DC DC DC SEQRES 1 G 18 DT DC DT DA RDG 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 RDG DG DG DT DC DC DT DA DG SEQRES 2 H 18 DG DA DC DC DC MODRES 4Q44 RDG B 841 DG MODRES 4Q44 RDG C 860 DG MODRES 4Q44 RDG G 841 DG MODRES 4Q44 RDG H 860 DG HET RDG B 841 28 HET RDG C 860 28 HET RDG G 841 28 HET RDG H 860 28 HET 1FZ A 401 29 HET MG A 402 1 HET MG A 403 1 HET 1FZ F 401 29 HET MG F 402 1 HET MG F 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 4(C15 H18 N5 O8 P) FORMUL 7 1FZ 2(C10 H18 N3 O13 P3) FORMUL 8 MG 4(MG 2+) FORMUL 13 HOH *87(H2 O) HELIX 1 1 CYS A 11 ASP A 20 1 10 HELIX 2 2 ASN A 45 LYS A 50 1 6 HELIX 3 3 PRO A 58 ALA A 64 1 7 HELIX 4 4 ARG A 75 ARG A 92 1 18 HELIX 5 5 SER A 118 GLN A 135 1 18 HELIX 6 6 VAL A 145 ASP A 154 1 10 HELIX 7 7 GLU A 168 THR A 175 1 8 HELIX 8 8 PRO A 177 ILE A 181 5 5 HELIX 9 9 GLY A 185 MET A 195 1 11 HELIX 10 10 THR A 199 ALA A 205 1 7 HELIX 11 11 ASP A 207 GLY A 216 1 10 HELIX 12 12 GLY A 216 GLN A 227 1 12 HELIX 13 13 HIS A 255 ALA A 275 1 21 HELIX 14 14 ASN A 308 ARG A 324 1 17 HELIX 15 15 CYS F 11 ASN F 21 1 11 HELIX 16 16 PRO F 22 ARG F 25 5 4 HELIX 17 17 ASN F 45 LYS F 50 1 6 HELIX 18 18 PRO F 58 CYS F 66 1 9 HELIX 19 19 ARG F 75 THR F 94 1 20 HELIX 20 20 SER F 118 GLN F 135 1 18 HELIX 21 21 VAL F 145 MET F 155 1 11 HELIX 22 22 GLU F 168 THR F 175 1 8 HELIX 23 23 PRO F 177 ILE F 181 5 5 HELIX 24 24 GLY F 185 ALA F 194 1 10 HELIX 25 25 THR F 199 ALA F 205 1 7 HELIX 26 26 ASP F 207 GLY F 216 1 10 HELIX 27 27 GLY F 216 GLN F 227 1 12 HELIX 28 28 HIS F 255 LYS F 278 1 24 HELIX 29 29 LYS F 309 ARG F 323 1 15 SHEET 1 A 5 ILE A 97 PRO A 99 0 SHEET 2 A 5 GLU A 104 ASP A 108 -1 O TYR A 106 N GLU A 98 SHEET 3 A 5 ILE A 4 MET A 9 -1 N VAL A 7 O ALA A 105 SHEET 4 A 5 ALA A 138 ALA A 143 -1 O ALA A 143 N ILE A 4 SHEET 5 A 5 GLN A 161 VAL A 163 1 O PHE A 162 N VAL A 142 SHEET 1 B 3 ILE A 41 ALA A 44 0 SHEET 2 B 3 ILE A 29 GLY A 32 -1 N ILE A 31 O SER A 42 SHEET 3 B 3 THR A 70 LEU A 72 1 O LEU A 72 N GLY A 32 SHEET 1 C 4 VAL A 243 THR A 248 0 SHEET 2 C 4 VAL A 329 VAL A 336 -1 O LEU A 334 N VAL A 245 SHEET 3 C 4 ARG A 285 PHE A 292 -1 N LYS A 289 O GLY A 333 SHEET 4 C 4 GLN A 297 VAL A 303 -1 O GLN A 300 N VAL A 288 SHEET 1 D 5 ILE F 97 PRO F 99 0 SHEET 2 D 5 GLU F 104 ASP F 108 -1 O TYR F 106 N GLU F 98 SHEET 3 D 5 ILE F 4 MET F 9 -1 N VAL F 7 O ALA F 105 SHEET 4 D 5 ALA F 138 ALA F 143 -1 O ALA F 143 N ILE F 4 SHEET 5 D 5 GLN F 161 VAL F 163 1 O PHE F 162 N VAL F 142 SHEET 1 E 3 ILE F 41 ALA F 44 0 SHEET 2 E 3 ILE F 29 GLY F 32 -1 N ILE F 31 O SER F 42 SHEET 3 E 3 THR F 70 LEU F 72 1 O LEU F 72 N ALA F 30 SHEET 1 F 4 SER F 242 ILE F 253 0 SHEET 2 F 4 VAL F 329 THR F 337 -1 O ARG F 330 N MET F 249 SHEET 3 F 4 ARG F 285 PHE F 292 -1 N GLY F 287 O HIS F 335 SHEET 4 F 4 GLN F 297 VAL F 303 -1 O HIS F 302 N GLN F 286 LINK O3' DA B 840 P RDG B 841 1555 1555 1.61 LINK O3' RDG B 841 P DG B 842 1555 1555 1.61 LINK O3' DA C 859 P RDG C 860 1555 1555 1.61 LINK O3' RDG C 860 P DG C 861 1555 1555 1.61 LINK O3' DA G 840 P RDG G 841 1555 1555 1.61 LINK O3' RDG G 841 P DG G 842 1555 1555 1.61 LINK O3' RDG H 860 P DG H 861 1555 1555 1.61 LINK OD1 ASP A 8 MG MG A 402 1555 1555 1.94 LINK OD2 ASP A 8 MG MG A 403 1555 1555 2.18 LINK O MET A 9 MG MG A 402 1555 1555 2.26 LINK OD2 ASP A 103 MG MG A 402 1555 1555 2.22 LINK OE2 GLU A 104 MG MG A 403 1555 1555 2.04 LINK O2B 1FZ A 401 MG MG A 402 1555 1555 2.02 LINK O1A 1FZ A 401 MG MG A 402 1555 1555 2.11 LINK O1G 1FZ A 401 MG MG A 402 1555 1555 2.69 LINK O1A 1FZ A 401 MG MG A 403 1555 1555 2.58 LINK MG MG A 403 O HOH A 502 1555 1555 2.85 LINK MG MG A 403 O HOH C 901 1555 1555 2.06 LINK OD1 ASP F 8 MG MG F 402 1555 1555 2.45 LINK O MET F 9 MG MG F 402 1555 1555 2.03 LINK OD2 ASP F 103 MG MG F 402 1555 1555 2.13 LINK OD1 ASP F 103 MG MG F 403 1555 1555 2.39 LINK OD2 ASP F 103 MG MG F 403 1555 1555 2.41 LINK OE2 GLU F 104 MG MG F 403 1555 1555 2.21 LINK O2B 1FZ F 401 MG MG F 402 1555 1555 2.03 LINK O2A 1FZ F 401 MG MG F 402 1555 1555 2.62 LINK O2A 1FZ F 401 MG MG F 403 1555 1555 2.43 LINK MG MG F 403 O3' DC H 873 1555 1555 2.68 CISPEP 1 LYS A 157 PRO A 158 0 0.84 CISPEP 2 LYS F 157 PRO F 158 0 -2.42 SITE 1 AC1 18 ASP A 8 MET A 9 ASP A 10 CYS A 11 SITE 2 AC1 18 PHE A 12 PHE A 13 SER A 42 THR A 43 SITE 3 AC1 18 ARG A 49 ASP A 103 GLU A 104 LYS A 157 SITE 4 AC1 18 MG A 402 MG A 403 HOH A 507 DA B 840 SITE 5 AC1 18 RDG B 841 DC C 873 SITE 1 AC2 5 ASP A 8 MET A 9 ASP A 103 1FZ A 401 SITE 2 AC2 5 MG A 403 SITE 1 AC3 6 ASP A 8 GLU A 104 1FZ A 401 MG A 402 SITE 2 AC3 6 HOH A 502 HOH C 901 SITE 1 AC4 19 ASP F 8 MET F 9 ASP F 10 CYS F 11 SITE 2 AC4 19 PHE F 12 PHE F 13 SER F 42 THR F 43 SITE 3 AC4 19 ARG F 49 ASP F 103 GLU F 104 LYS F 157 SITE 4 AC4 19 MG F 402 MG F 403 HOH F 524 HOH F 529 SITE 5 AC4 19 DA G 840 RDG G 841 DC H 873 SITE 1 AC5 5 ASP F 8 MET F 9 ASP F 103 1FZ F 401 SITE 2 AC5 5 MG F 403 SITE 1 AC6 6 ASP F 8 ASP F 103 GLU F 104 1FZ F 401 SITE 2 AC6 6 MG F 402 DC H 873 CRYST1 86.655 56.934 110.396 90.00 94.66 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 0.011540 0.000000 0.000940 0.00000 SCALE2 0.000000 0.017564 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009088 0.00000