HEADER TRANSFERASE/DNA 23-JAN-12 4DF4 TITLE CRYSTAL STRUCTURE OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM TITLE 2 THERMUS AQUATICUS IN A CLOSED TERNARY COMPLEX WITH 7-(N-(10- TITLE 3 HYDROXYDECANOYL)-AMINOPENTINYL)-7-DEAZA-2 -DATP COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE I, THERMOSTABLE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: KLENOW FRAGMENT; COMPND 5 SYNONYM: TAQ POLYMERASE 1; COMPND 6 EC: 2.7.7.7; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3'); COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: DNA PRIMER; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: DNA (5'-D(*AP*AP*AP*TP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)- COMPND 15 3'); COMPND 16 CHAIN: C; COMPND 17 FRAGMENT: DNA TEMPLATE; COMPND 18 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS AQUATICUS; SOURCE 3 ORGANISM_TAXID: 271; SOURCE 4 GENE: POL I, POL1, POLA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21-DE3; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PET SERIES; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET21B; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES KEYWDS DNA POLYMERASE, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.BERGEN,A.STECK,S.STRUETT,A.BACCARO,W.WELTE,K.DIEDERICHS,A.MARX REVDAT 3 13-SEP-23 4DF4 1 REMARK LINK REVDAT 2 08-AUG-12 4DF4 1 JRNL REVDAT 1 16-MAY-12 4DF4 0 JRNL AUTH K.BERGEN,A.L.STECK,S.STRUTT,A.BACCARO,W.WELTE,K.DIEDERICHS, JRNL AUTH 2 A.MARX JRNL TITL STRUCTURES OF KLENTAQ DNA POLYMERASE CAUGHT WHILE JRNL TITL 2 INCORPORATING C5-MODIFIED PYRIMIDINE AND C7-MODIFIED JRNL TITL 3 7-DEAZAPURINE NUCLEOSIDE TRIPHOSPHATES. JRNL REF J.AM.CHEM.SOC. V. 134 11840 2012 JRNL REFN ISSN 0002-7863 JRNL PMID 22475415 JRNL DOI 10.1021/JA3017889 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.3_928) 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.20 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 30932 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 1568 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 46.2126 - 4.8912 1.00 2803 161 0.1661 0.2047 REMARK 3 2 4.8912 - 3.8830 1.00 2707 141 0.1414 0.1795 REMARK 3 3 3.8830 - 3.3923 1.00 2669 159 0.1600 0.2038 REMARK 3 4 3.3923 - 3.0822 1.00 2658 149 0.1869 0.2294 REMARK 3 5 3.0822 - 2.8613 1.00 2671 134 0.1983 0.2503 REMARK 3 6 2.8613 - 2.6926 1.00 2647 137 0.2035 0.2562 REMARK 3 7 2.6926 - 2.5578 1.00 2621 150 0.1989 0.2865 REMARK 3 8 2.5578 - 2.4465 1.00 2661 150 0.2036 0.2643 REMARK 3 9 2.4465 - 2.3523 1.00 2640 123 0.2123 0.3201 REMARK 3 10 2.3523 - 2.2711 1.00 2665 126 0.2080 0.2462 REMARK 3 11 2.2711 - 2.2001 1.00 2622 138 0.2139 0.2899 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.98 REMARK 3 K_SOL : 0.32 REMARK 3 B_SOL : 14.87 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.420 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.27 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 13.29400 REMARK 3 B22 (A**2) : 13.29400 REMARK 3 B33 (A**2) : 8.06780 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 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 : 0.011 5048 REMARK 3 ANGLE : 0.821 6966 REMARK 3 CHIRALITY : 0.046 759 REMARK 3 PLANARITY : 0.003 811 REMARK 3 DIHEDRAL : 15.228 1958 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 294:433) REMARK 3 ORIGIN FOR THE GROUP (A): 39.9181 -42.8681 -17.8547 REMARK 3 T TENSOR REMARK 3 T11: 0.0792 T22: 0.0183 REMARK 3 T33: 0.1340 T12: 0.0195 REMARK 3 T13: 0.0006 T23: 0.0223 REMARK 3 L TENSOR REMARK 3 L11: 0.0676 L22: 0.0319 REMARK 3 L33: 0.0761 L12: 0.0261 REMARK 3 L13: -0.0085 L23: -0.0140 REMARK 3 S TENSOR REMARK 3 S11: -0.0182 S12: -0.0025 S13: -0.1523 REMARK 3 S21: -0.0822 S22: -0.0021 S23: -0.1150 REMARK 3 S31: 0.1260 S32: 0.0419 S33: -0.0163 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 434:633) REMARK 3 ORIGIN FOR THE GROUP (A): 31.7371 -13.5691 -3.2747 REMARK 3 T TENSOR REMARK 3 T11: -0.0420 T22: -0.0499 REMARK 3 T33: 0.0281 T12: -0.1268 REMARK 3 T13: 0.0589 T23: 0.0293 REMARK 3 L TENSOR REMARK 3 L11: 0.0885 L22: 0.0539 REMARK 3 L33: 0.0440 L12: 0.0730 REMARK 3 L13: -0.0218 L23: -0.0453 REMARK 3 S TENSOR REMARK 3 S11: 0.0546 S12: -0.0460 S13: 0.0966 REMARK 3 S21: 0.0546 S22: -0.0470 S23: -0.0131 REMARK 3 S31: -0.0365 S32: -0.0631 S33: 0.0029 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 634:737) REMARK 3 ORIGIN FOR THE GROUP (A): 9.4136 -21.3680 -2.4503 REMARK 3 T TENSOR REMARK 3 T11: 0.2168 T22: 0.2192 REMARK 3 T33: 0.1004 T12: 0.0699 REMARK 3 T13: 0.0179 T23: 0.0209 REMARK 3 L TENSOR REMARK 3 L11: 0.0466 L22: 0.0062 REMARK 3 L33: 0.0397 L12: -0.0121 REMARK 3 L13: 0.0153 L23: 0.0072 REMARK 3 S TENSOR REMARK 3 S11: -0.0194 S12: -0.1270 S13: 0.0367 REMARK 3 S21: 0.0627 S22: 0.0555 S23: 0.0286 REMARK 3 S31: -0.1540 S32: -0.2240 S33: -0.0119 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 738:832) REMARK 3 ORIGIN FOR THE GROUP (A): 22.6604 -21.3904 -19.8321 REMARK 3 T TENSOR REMARK 3 T11: 0.0222 T22: 0.0395 REMARK 3 T33: 0.0238 T12: -0.0125 REMARK 3 T13: -0.0184 T23: 0.0097 REMARK 3 L TENSOR REMARK 3 L11: 0.0747 L22: 0.0989 REMARK 3 L33: 0.1598 L12: -0.0309 REMARK 3 L13: 0.0513 L23: 0.0772 REMARK 3 S TENSOR REMARK 3 S11: 0.0111 S12: -0.0310 S13: -0.0275 REMARK 3 S21: -0.0805 S22: 0.0400 S23: 0.0025 REMARK 3 S31: -0.0594 S32: -0.0956 S33: 0.0778 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 4DF4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-FEB-12. REMARK 100 THE DEPOSITION ID IS D_1000070250. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAY-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 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) : 1.000000 REMARK 200 MONOCHROMATOR : BARTELS MONOCHROMATOR SI (111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41455 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.990 REMARK 200 RESOLUTION RANGE LOW (A) : 46.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 11.09 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.8700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.99 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.640 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: DIFFERENCE FOURIER REMARK 200 TECHNIQUES REMARK 200 SOFTWARE USED: PHENIX 1.7.3_928 REMARK 200 STARTING MODEL: PDB ENTRY 3M8S REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18% PEG 8000, 200MM MG-FORMATE, 100 REMARK 280 MMTRIS PH 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 29.89267 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 59.78533 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 59.78533 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 29.89267 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: 5720 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -37.0 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 A1225 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1296 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 ALA A 293 REMARK 465 DA C 201 REMARK 465 DA C 202 REMARK 465 DA C 203 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 ARG A 556 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 832 CG CD OE1 OE2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 VAL A 307 CA CB CG1 CG2 REMARK 480 LYS A 346 CG CD CE NZ REMARK 480 GLU A 524 C OE1 OE2 REMARK 480 MET A 751 CA CB CG SD CE 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 B 109 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DOC B 112 O3' - P - OP1 ANGL. DEV. = -22.3 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 ASP A 381 112.37 -160.16 REMARK 500 VAL A 433 -75.24 -117.12 REMARK 500 ASP A 496 -64.33 -92.60 REMARK 500 VAL A 586 -13.65 -158.57 REMARK 500 HIS A 784 -64.50 70.53 REMARK 500 TYR A 811 87.49 -160.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 0L3 A 903 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 901 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 610 OD1 REMARK 620 2 TYR A 611 O 85.0 REMARK 620 3 ASP A 785 OD2 96.6 101.5 REMARK 620 4 0L3 A 903 O3G 105.9 86.8 156.7 REMARK 620 5 0L3 A 903 O2B 177.7 96.5 84.9 72.4 REMARK 620 6 0L3 A 903 O2A 108.0 167.0 76.4 90.6 70.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 902 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 610 OD2 REMARK 620 2 ASP A 610 OD1 47.9 REMARK 620 3 ASP A 785 OD1 115.6 81.2 REMARK 620 4 0L3 A 903 O2A 112.9 78.0 84.8 REMARK 620 5 HOH A1287 O 95.0 125.5 149.2 86.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 905 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A1295 O REMARK 620 2 HOH A1296 O 179.9 REMARK 620 3 HOH A1297 O 90.1 90.0 REMARK 620 4 HOH A1298 O 90.0 90.0 90.0 REMARK 620 5 HOH A1299 O 90.0 90.0 90.0 180.0 REMARK 620 6 HOH A1300 O 89.9 90.0 179.9 90.1 89.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 906 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A1172 O REMARK 620 2 HOH A1174 O 68.9 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 320 O REMARK 620 2 HOH B 321 O 179.8 REMARK 620 3 HOH B 322 O 89.9 89.9 REMARK 620 4 HOH B 323 O 89.9 89.9 90.0 REMARK 620 5 HOH B 324 O 90.1 90.1 89.9 180.0 REMARK 620 6 HOH C 332 O 90.1 90.0 179.9 90.1 90.0 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 MG A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 0L3 A 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 904 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 905 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 906 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3KTQ RELATED DB: PDB REMARK 900 RELATED ID: 3OJU RELATED DB: PDB REMARK 900 RELATED ID: 3OJS RELATED DB: PDB REMARK 900 RELATED ID: 3LWM RELATED DB: PDB REMARK 900 RELATED ID: 3LWL RELATED DB: PDB REMARK 900 RELATED ID: 3M8S RELATED DB: PDB DBREF 4DF4 A 293 832 UNP P19821 DPO1_THEAQ 293 832 DBREF 4DF4 B 101 112 PDB 4DF4 4DF4 101 112 DBREF 4DF4 C 201 216 PDB 4DF4 4DF4 201 216 SEQRES 1 A 540 ALA LEU GLU GLU ALA PRO TRP PRO PRO PRO GLU GLY ALA SEQRES 2 A 540 PHE VAL GLY PHE VAL LEU SER ARG LYS GLU PRO MET TRP SEQRES 3 A 540 ALA ASP LEU LEU ALA LEU ALA ALA ALA ARG GLY GLY ARG SEQRES 4 A 540 VAL HIS ARG ALA PRO GLU PRO TYR LYS ALA LEU ARG ASP SEQRES 5 A 540 LEU LYS GLU ALA ARG GLY LEU LEU ALA LYS ASP LEU SER SEQRES 6 A 540 VAL LEU ALA LEU ARG GLU GLY LEU GLY LEU PRO PRO GLY SEQRES 7 A 540 ASP ASP PRO MET LEU LEU ALA TYR LEU LEU ASP PRO SER SEQRES 8 A 540 ASN THR THR PRO GLU GLY VAL ALA ARG ARG TYR GLY GLY SEQRES 9 A 540 GLU TRP THR GLU GLU ALA GLY GLU ARG ALA ALA LEU SER SEQRES 10 A 540 GLU ARG LEU PHE ALA ASN LEU TRP GLY ARG LEU GLU GLY SEQRES 11 A 540 GLU GLU ARG LEU LEU TRP LEU TYR ARG GLU VAL GLU ARG SEQRES 12 A 540 PRO LEU SER ALA VAL LEU ALA HIS MET GLU ALA THR GLY SEQRES 13 A 540 VAL ARG LEU ASP VAL ALA TYR LEU ARG ALA LEU SER LEU SEQRES 14 A 540 GLU VAL ALA GLU GLU ILE ALA ARG LEU GLU ALA GLU VAL SEQRES 15 A 540 PHE ARG LEU ALA GLY HIS PRO PHE ASN LEU ASN SER ARG SEQRES 16 A 540 ASP GLN LEU GLU ARG VAL LEU PHE ASP GLU LEU GLY LEU SEQRES 17 A 540 PRO ALA ILE GLY LYS THR GLU LYS THR GLY LYS ARG SER SEQRES 18 A 540 THR SER ALA ALA VAL LEU GLU ALA LEU ARG GLU ALA HIS SEQRES 19 A 540 PRO ILE VAL GLU LYS ILE LEU GLN TYR ARG GLU LEU THR SEQRES 20 A 540 LYS LEU LYS SER THR TYR ILE ASP PRO LEU PRO ASP LEU SEQRES 21 A 540 ILE HIS PRO ARG THR GLY ARG LEU HIS THR ARG PHE ASN SEQRES 22 A 540 GLN THR ALA THR ALA THR GLY ARG LEU SER SER SER ASP SEQRES 23 A 540 PRO ASN LEU GLN ASN ILE PRO VAL ARG THR PRO LEU GLY SEQRES 24 A 540 GLN ARG ILE ARG ARG ALA PHE ILE ALA GLU GLU GLY TRP SEQRES 25 A 540 LEU LEU VAL ALA LEU ASP TYR SER GLN ILE GLU LEU ARG SEQRES 26 A 540 VAL LEU ALA HIS LEU SER GLY ASP GLU ASN LEU ILE ARG SEQRES 27 A 540 VAL PHE GLN GLU GLY ARG ASP ILE HIS THR GLU THR ALA SEQRES 28 A 540 SER TRP MET PHE GLY VAL PRO ARG GLU ALA VAL ASP PRO SEQRES 29 A 540 LEU MET ARG ARG ALA ALA LYS THR ILE ASN PHE GLY VAL SEQRES 30 A 540 LEU TYR GLY MET SER ALA HIS ARG LEU SER GLN GLU LEU SEQRES 31 A 540 ALA ILE PRO TYR GLU GLU ALA GLN ALA PHE ILE GLU ARG SEQRES 32 A 540 TYR PHE GLN SER PHE PRO LYS VAL ARG ALA TRP ILE GLU SEQRES 33 A 540 LYS THR LEU GLU GLU GLY ARG ARG ARG GLY TYR VAL GLU SEQRES 34 A 540 THR LEU PHE GLY ARG ARG ARG TYR VAL PRO ASP LEU GLU SEQRES 35 A 540 ALA ARG VAL LYS SER VAL ARG GLU ALA ALA GLU ARG MET SEQRES 36 A 540 ALA PHE ASN MET PRO VAL GLN GLY THR ALA ALA ASP LEU SEQRES 37 A 540 MET LYS LEU ALA MET VAL LYS LEU PHE PRO ARG LEU GLU SEQRES 38 A 540 GLU MET GLY ALA ARG MET LEU LEU GLN VAL HIS ASP GLU SEQRES 39 A 540 LEU VAL LEU GLU ALA PRO LYS GLU ARG ALA GLU ALA VAL SEQRES 40 A 540 ALA ARG LEU ALA LYS GLU VAL MET GLU GLY VAL TYR PRO SEQRES 41 A 540 LEU ALA VAL PRO LEU GLU VAL GLU VAL GLY ILE GLY GLU SEQRES 42 A 540 ASP TRP LEU SER ALA LYS GLU SEQRES 1 B 12 DG DA DC DC DA DC DG DG DC DG DC DOC SEQRES 1 C 16 DA DA DA DT DG DG DC DG DC DC DG DT DG SEQRES 2 C 16 DG DT DC MODRES 4DF4 DOC B 112 DC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HET DOC B 112 18 HET MG A 901 1 HET MG A 902 1 HET 0L3 A 903 48 HET EDO A 904 4 HET MG A 905 1 HET MG A 906 1 HET MG B 201 1 HETNAM DOC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM 0L3 7-{2-DEOXY-5-O-[(S)-HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY) HETNAM 2 0L3 PHOSPHORYL]OXY}PHOSPHORYL]-BETA-D-ERYTHRO- HETNAM 3 0L3 PENTOFURANOSYL}-5-{5-[(10-HYDROXYDECANOYL)AMINO]PENT- HETNAM 4 0L3 1-YN-1-YL}-7H-PYRROLO[2,3-D]PYRIMIDIN-4-AMINE HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 DOC C9 H14 N3 O6 P FORMUL 4 MG 5(MG 2+) FORMUL 6 0L3 C26 H42 N5 O14 P3 FORMUL 7 EDO C2 H6 O2 FORMUL 11 HOH *356(H2 O) HELIX 1 1 GLU A 337 LEU A 342 1 6 HELIX 2 2 ARG A 343 LEU A 345 5 3 HELIX 3 3 LEU A 352 GLU A 363 1 12 HELIX 4 4 ASP A 372 ASP A 381 1 10 HELIX 5 5 THR A 386 GLY A 395 1 10 HELIX 6 6 GLU A 401 LEU A 420 1 20 HELIX 7 7 GLU A 423 VAL A 433 1 11 HELIX 8 8 VAL A 433 GLY A 448 1 16 HELIX 9 9 ASP A 452 GLY A 479 1 28 HELIX 10 10 SER A 486 ASP A 496 1 11 HELIX 11 11 SER A 515 ALA A 521 1 7 HELIX 12 12 HIS A 526 TYR A 545 1 20 HELIX 13 13 PRO A 548 ILE A 553 5 6 HELIX 14 14 THR A 588 ARG A 596 1 9 HELIX 15 15 GLN A 613 GLY A 624 1 12 HELIX 16 16 ASP A 625 GLU A 634 1 10 HELIX 17 17 ASP A 637 GLY A 648 1 12 HELIX 18 18 PRO A 650 VAL A 654 5 5 HELIX 19 19 ASP A 655 TYR A 671 1 17 HELIX 20 20 SER A 674 ALA A 683 1 10 HELIX 21 21 PRO A 685 SER A 699 1 15 HELIX 22 22 PHE A 700 GLY A 718 1 19 HELIX 23 23 PRO A 731 ALA A 735 5 5 HELIX 24 24 VAL A 737 MET A 775 1 39 HELIX 25 25 ARG A 795 GLY A 809 1 15 SHEET 1 A 4 GLU A 295 ALA A 297 0 SHEET 2 A 4 ARG A 331 ARG A 334 1 O VAL A 332 N ALA A 297 SHEET 3 A 4 LEU A 321 ARG A 328 -1 N ALA A 326 O HIS A 333 SHEET 4 A 4 PHE A 306 LEU A 311 -1 N GLY A 308 O ALA A 325 SHEET 1 B 2 ARG A 450 LEU A 451 0 SHEET 2 B 2 PHE A 598 ILE A 599 -1 O ILE A 599 N ARG A 450 SHEET 1 C 2 ARG A 563 ASN A 565 0 SHEET 2 C 2 SER A 575 SER A 577 -1 O SER A 575 N ASN A 565 SHEET 1 D 4 ARG A 778 GLN A 782 0 SHEET 2 D 4 GLU A 786 PRO A 792 -1 O GLU A 790 N ARG A 778 SHEET 3 D 4 TRP A 604 TYR A 611 -1 N VAL A 607 O LEU A 789 SHEET 4 D 4 VAL A 819 GLY A 824 -1 O GLU A 820 N ASP A 610 SHEET 1 E 2 TYR A 719 GLU A 721 0 SHEET 2 E 2 ARG A 727 TYR A 729 -1 O ARG A 728 N VAL A 720 LINK O3' DC B 111 P DOC B 112 1555 1555 1.60 LINK OD1AASP A 610 MG MG A 901 1555 1555 1.97 LINK OD2AASP A 610 MG MG A 902 1555 1555 2.19 LINK OD1AASP A 610 MG MG A 902 1555 1555 2.92 LINK O TYR A 611 MG MG A 901 1555 1555 1.96 LINK OD2 ASP A 785 MG MG A 901 1555 1555 2.04 LINK OD1 ASP A 785 MG MG A 902 1555 1555 2.14 LINK MG MG A 901 O3G 0L3 A 903 1555 1555 2.00 LINK MG MG A 901 O2B 0L3 A 903 1555 1555 2.06 LINK MG MG A 901 O2A 0L3 A 903 1555 1555 2.10 LINK MG MG A 902 O2A 0L3 A 903 1555 1555 2.24 LINK MG MG A 902 O HOH A1287 1555 1555 2.81 LINK MG MG A 905 O HOH A1295 1555 1555 2.18 LINK MG MG A 905 O HOH A1296 1555 1555 2.18 LINK MG MG A 905 O HOH A1297 1555 1555 2.18 LINK MG MG A 905 O HOH A1298 1555 1555 2.18 LINK MG MG A 905 O HOH A1299 1555 1555 2.18 LINK MG MG A 905 O HOH A1300 1555 1555 2.18 LINK MG MG A 906 O HOH A1172 1555 1555 2.07 LINK MG MG A 906 O HOH A1174 1555 1555 2.08 LINK MG MG B 201 O HOH B 320 1555 1555 2.18 LINK MG MG B 201 O HOH B 321 1555 1555 2.18 LINK MG MG B 201 O HOH B 322 1555 1555 2.18 LINK MG MG B 201 O HOH B 323 1555 1555 2.18 LINK MG MG B 201 O HOH B 324 1555 1555 2.18 LINK MG MG B 201 O HOH C 332 1555 1555 2.18 CISPEP 1 TRP A 299 PRO A 300 0 1.58 CISPEP 2 ASP A 578 PRO A 579 0 -2.43 SITE 1 AC1 5 ASP A 610 TYR A 611 ASP A 785 MG A 902 SITE 2 AC1 5 0L3 A 903 SITE 1 AC2 8 ASP A 610 ASP A 785 GLU A 786 MG A 901 SITE 2 AC2 8 0L3 A 903 HOH A1279 HOH A1287 DOC B 112 SITE 1 AC3 21 ARG A 573 ASP A 610 TYR A 611 SER A 612 SITE 2 AC3 21 GLN A 613 ILE A 614 GLU A 615 HIS A 639 SITE 3 AC3 21 ARG A 659 ARG A 660 LYS A 663 PHE A 667 SITE 4 AC3 21 ASP A 785 MG A 901 MG A 902 HOH A1123 SITE 5 AC3 21 HOH A1147 HOH A1287 DOC B 112 DT C 204 SITE 6 AC3 21 DG C 205 SITE 1 AC4 4 LYS A 314 ASP A 578 DC C 209 HOH C 316 SITE 1 AC5 6 HOH A1295 HOH A1296 HOH A1297 HOH A1298 SITE 2 AC5 6 HOH A1299 HOH A1300 SITE 1 AC6 3 TRP A 318 HOH A1172 HOH A1174 SITE 1 AC7 6 HOH B 320 HOH B 321 HOH B 322 HOH B 323 SITE 2 AC7 6 HOH B 324 HOH C 332 CRYST1 107.815 107.815 89.678 90.00 90.00 120.00 P 31 2 1 6 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 0.009275 0.005355 0.000000 0.00000 SCALE2 0.000000 0.010710 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011151 0.00000