HEADER TRANSFERASE/DNA 22-NOV-10 3PO4 TITLE STRUCTURE OF A MUTANT OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM TITLE 2 THERMUS AQUATICUS IN COMPLEX WITH A BLUNT-ENDED DNA AND DDATP COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE I; 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 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(2DA))-3'); COMPND 11 CHAIN: B; COMPND 12 FRAGMENT: DNA PRIMER; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: DNA (5'-D(*TP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-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: POL1, POLA, POLI; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21DE3; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-21B; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES KEYWDS DNA POLYMERASE, BLUNT-ENDED DNA, PROCESSING AN A-OVERHANG, DNA KEYWDS 2 PRIMER/TEMPLATE DUPLEX, DDATP, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.MARX,K.DIEDERICHS,S.OBEID REVDAT 4 06-SEP-23 3PO4 1 REMARK SEQADV LINK REVDAT 3 08-NOV-17 3PO4 1 REMARK REVDAT 2 13-JUL-11 3PO4 1 JRNL REVDAT 1 15-JUN-11 3PO4 0 JRNL AUTH S.OBEID,A.SCHNUR,C.GLOECKNER,N.BLATTER,W.WELTE,K.DIEDERICHS, JRNL AUTH 2 A.MARX JRNL TITL LEARNING FROM DIRECTED EVOLUTION: THERMUS AQUATICUS DNA JRNL TITL 2 POLYMERASE MUTANTS WITH TRANSLESION SYNTHESIS ACTIVITY. JRNL REF CHEMBIOCHEM V. 12 1574 2011 JRNL REFN ISSN 1439-4227 JRNL PMID 21480455 JRNL DOI 10.1002/CBIC.201000783 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: DEV_572) 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.20 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.050 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 63101 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970 REMARK 3 FREE R VALUE TEST SET COUNT : 3133 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 48.2137 - 5.0418 1.00 2879 164 0.1707 0.1958 REMARK 3 2 5.0418 - 4.0025 1.00 2777 151 0.1240 0.1375 REMARK 3 3 4.0025 - 3.4967 1.00 2745 163 0.1535 0.1723 REMARK 3 4 3.4967 - 3.1771 1.00 2741 146 0.1719 0.1981 REMARK 3 5 3.1771 - 2.9494 1.00 2752 145 0.1812 0.1957 REMARK 3 6 2.9494 - 2.7755 1.00 2739 131 0.1812 0.2219 REMARK 3 7 2.7755 - 2.6365 1.00 2703 156 0.1751 0.2160 REMARK 3 8 2.6365 - 2.5218 1.00 2703 159 0.1750 0.2112 REMARK 3 9 2.5218 - 2.4247 1.00 2739 129 0.1592 0.2185 REMARK 3 10 2.4247 - 2.3410 1.00 2740 124 0.1657 0.1853 REMARK 3 11 2.3410 - 2.2678 1.00 2717 137 0.1591 0.2130 REMARK 3 12 2.2678 - 2.2030 1.00 2737 121 0.1609 0.1865 REMARK 3 13 2.2030 - 2.1450 1.00 2687 136 0.1578 0.2200 REMARK 3 14 2.1450 - 2.0927 1.00 2696 155 0.1678 0.2041 REMARK 3 15 2.0927 - 2.0451 1.00 2725 128 0.1724 0.2390 REMARK 3 16 2.0451 - 2.0016 1.00 2733 120 0.1795 0.1992 REMARK 3 17 2.0016 - 1.9615 1.00 2702 141 0.1830 0.2614 REMARK 3 18 1.9615 - 1.9245 1.00 2677 156 0.1929 0.2427 REMARK 3 19 1.9245 - 1.8901 1.00 2681 139 0.1860 0.2487 REMARK 3 20 1.8901 - 1.8581 1.00 2729 140 0.2030 0.2607 REMARK 3 21 1.8581 - 1.8281 1.00 2694 152 0.2083 0.2570 REMARK 3 22 1.8281 - 1.8000 1.00 2672 140 0.2339 0.2501 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 : 0.36 REMARK 3 B_SOL : 42.38 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 42.02 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.69160 REMARK 3 B22 (A**2) : 4.69160 REMARK 3 B33 (A**2) : -0.43330 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 : 0.007 5006 REMARK 3 ANGLE : 1.088 6906 REMARK 3 CHIRALITY : 0.062 742 REMARK 3 PLANARITY : 0.005 811 REMARK 3 DIHEDRAL : 17.399 1970 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 295:446) REMARK 3 ORIGIN FOR THE GROUP (A): 41.7193 -44.3751 -18.4385 REMARK 3 T TENSOR REMARK 3 T11: 0.2984 T22: 0.1900 REMARK 3 T33: 0.2723 T12: 0.0664 REMARK 3 T13: 0.0605 T23: 0.0469 REMARK 3 L TENSOR REMARK 3 L11: 1.2664 L22: 0.8682 REMARK 3 L33: 0.6816 L12: -0.1573 REMARK 3 L13: 0.0849 L23: 0.0460 REMARK 3 S TENSOR REMARK 3 S11: 0.0824 S12: 0.0598 S13: -0.2851 REMARK 3 S21: -0.2284 S22: -0.1756 S23: -0.1222 REMARK 3 S31: 0.3436 S32: 0.1171 S33: 0.0507 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 447:644) REMARK 3 ORIGIN FOR THE GROUP (A): 31.7889 -15.0293 -2.8340 REMARK 3 T TENSOR REMARK 3 T11: 0.2236 T22: 0.1927 REMARK 3 T33: 0.2564 T12: -0.0137 REMARK 3 T13: 0.0088 T23: 0.0242 REMARK 3 L TENSOR REMARK 3 L11: 0.5089 L22: 0.8770 REMARK 3 L33: 1.3653 L12: 0.0736 REMARK 3 L13: 0.2253 L23: -0.1616 REMARK 3 S TENSOR REMARK 3 S11: -0.0135 S12: -0.0358 S13: 0.1835 REMARK 3 S21: 0.1075 S22: -0.0803 S23: -0.0653 REMARK 3 S31: -0.2710 S32: -0.0431 S33: 0.0652 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 645:671) REMARK 3 ORIGIN FOR THE GROUP (A): 9.6305 -13.0982 -5.2590 REMARK 3 T TENSOR REMARK 3 T11: 0.5406 T22: 0.4839 REMARK 3 T33: 0.2485 T12: 0.2123 REMARK 3 T13: 0.0698 T23: -0.0230 REMARK 3 L TENSOR REMARK 3 L11: 3.5524 L22: 0.3898 REMARK 3 L33: 0.6846 L12: 0.5364 REMARK 3 L13: -0.1648 L23: 0.3674 REMARK 3 S TENSOR REMARK 3 S11: 0.0369 S12: -0.2339 S13: -0.1609 REMARK 3 S21: 0.1954 S22: 0.1751 S23: -0.0577 REMARK 3 S31: -1.0520 S32: -0.4394 S33: -0.1661 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 672:701) REMARK 3 ORIGIN FOR THE GROUP (A): 9.0121 -19.4384 4.4694 REMARK 3 T TENSOR REMARK 3 T11: 0.3459 T22: 0.6366 REMARK 3 T33: 0.2952 T12: 0.0800 REMARK 3 T13: -0.0017 T23: -0.0779 REMARK 3 L TENSOR REMARK 3 L11: 1.6471 L22: 1.7747 REMARK 3 L33: 1.2247 L12: -0.1447 REMARK 3 L13: -1.2634 L23: -0.5414 REMARK 3 S TENSOR REMARK 3 S11: 0.1196 S12: -0.0576 S13: 0.0334 REMARK 3 S21: 0.2950 S22: -0.0616 S23: 0.0982 REMARK 3 S31: -0.1362 S32: 0.1487 S33: -0.0525 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN A AND RESID 702:832) REMARK 3 ORIGIN FOR THE GROUP (A): 21.4677 -28.9782 -15.6872 REMARK 3 T TENSOR REMARK 3 T11: 0.1950 T22: 0.2186 REMARK 3 T33: 0.1808 T12: -0.0118 REMARK 3 T13: 0.0031 T23: 0.0254 REMARK 3 L TENSOR REMARK 3 L11: 1.2636 L22: 0.6635 REMARK 3 L33: 1.4404 L12: 0.0848 REMARK 3 L13: -0.1257 L23: -0.2969 REMARK 3 S TENSOR REMARK 3 S11: 0.0008 S12: 0.1091 S13: -0.0116 REMARK 3 S21: -0.1529 S22: -0.0137 S23: 0.0078 REMARK 3 S31: 0.1250 S32: -0.2189 S33: 0.0044 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN B) REMARK 3 ORIGIN FOR THE GROUP (A): 38.7643 -25.3163 4.0290 REMARK 3 T TENSOR REMARK 3 T11: 0.1915 T22: 0.2601 REMARK 3 T33: 0.2512 T12: 0.0114 REMARK 3 T13: -0.0423 T23: 0.0353 REMARK 3 L TENSOR REMARK 3 L11: 0.6506 L22: 1.3086 REMARK 3 L33: 0.4884 L12: 0.4291 REMARK 3 L13: 0.3537 L23: -0.0800 REMARK 3 S TENSOR REMARK 3 S11: 0.0118 S12: 0.0966 S13: -0.0450 REMARK 3 S21: 0.2851 S22: -0.0661 S23: -0.1284 REMARK 3 S31: -0.1514 S32: 0.0696 S33: -0.0058 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN C) REMARK 3 ORIGIN FOR THE GROUP (A): 40.0945 -26.2970 5.4174 REMARK 3 T TENSOR REMARK 3 T11: 0.1816 T22: 0.2395 REMARK 3 T33: 0.2416 T12: 0.0178 REMARK 3 T13: -0.0692 T23: 0.0351 REMARK 3 L TENSOR REMARK 3 L11: 0.6053 L22: 0.3920 REMARK 3 L33: 0.3104 L12: 0.1286 REMARK 3 L13: 0.1290 L23: 0.2238 REMARK 3 S TENSOR REMARK 3 S11: -0.1015 S12: 0.1081 S13: -0.0737 REMARK 3 S21: 0.0991 S22: 0.1040 S23: -0.1699 REMARK 3 S31: 0.0974 S32: 0.0844 S33: -0.0048 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 3PO4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-DEC-10. REMARK 100 THE DEPOSITION ID IS D_1000062611. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-MAY-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : LN2 COOLED FIXED-EXIT, SI(111) REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : DYNAMICALLY BENDABLE MIRROR, LN2 REMARK 200 COOLED FIXED-EXIT, SI(111) REMARK 200 MONOCHROMATOR REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 63101 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 9.960 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.8800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.91 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5 REMARK 200 DATA REDUNDANCY IN SHELL : 10.08 REMARK 200 R MERGE FOR SHELL (I) : 0.76700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.630 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX DEV_572 REMARK 200 STARTING MODEL: PDB ENTRY 3LWM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05M SODIUM CACODYLATE, 0.2M KCL, REMARK 280 0.1M MG(OAC)2, 20% PEG 8000, PH 7.0, VAPOR DIFFUSION, HANGING REMARK 280 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 30.41267 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 60.82533 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 60.82533 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 30.41267 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: 5460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -45.0 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 ALA A 293 REMARK 465 LEU A 294 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 HOH A 851 O HOH A 1021 1.76 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 C 205 O4' DT C 205 C1' 0.066 REMARK 500 DT C 205 N1 DT C 205 C2 0.051 REMARK 500 DT C 205 C5 DT C 205 C6 0.082 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 B 106 O4' - C1' - N1 ANGL. DEV. = -5.6 DEGREES REMARK 500 DG B 107 O4' - C1' - N9 ANGL. DEV. = -4.5 DEGREES REMARK 500 DG B 108 C1' - O4' - C4' ANGL. DEV. = -6.3 DEGREES REMARK 500 DG B 108 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 DC B 109 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 DT C 205 C5' - C4' - O4' ANGL. DEV. = 6.6 DEGREES REMARK 500 DT C 205 N1 - C1' - C2' ANGL. DEV. = 12.8 DEGREES REMARK 500 DT C 205 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DT C 205 N1 - C2 - N3 ANGL. DEV. = 3.8 DEGREES REMARK 500 DT C 205 C2 - N3 - C4 ANGL. DEV. = -6.3 DEGREES REMARK 500 DT C 205 N3 - C4 - C5 ANGL. DEV. = 5.2 DEGREES REMARK 500 DT C 205 C5 - C6 - N1 ANGL. DEV. = -4.8 DEGREES REMARK 500 DT C 205 N1 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 DG C 211 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DG C 214 O4' - C1' - N9 ANGL. DEV. = 2.9 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 381 113.26 -169.89 REMARK 500 THR A 399 -168.94 -107.02 REMARK 500 ILE A 503 -76.56 -75.05 REMARK 500 HIS A 526 139.23 -178.58 REMARK 500 TYR A 545 -56.83 -121.70 REMARK 500 VAL A 586 -16.35 -154.75 REMARK 500 PHE A 647 -150.10 -113.51 REMARK 500 VAL A 649 -174.75 57.63 REMARK 500 HIS A 784 -62.35 73.10 REMARK 500 TYR A 811 100.44 -163.73 REMARK 500 LYS A 831 91.14 -62.18 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 1 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 19 O REMARK 620 2 DDS A 835 O2A 170.8 REMARK 620 3 DDS A 835 O2B 88.7 83.1 REMARK 620 4 DDS A 835 O3G 86.2 88.9 85.6 REMARK 620 5 HOH A 842 O 92.1 92.3 91.0 176.3 REMARK 620 6 HOH A 851 O 72.1 115.9 160.7 91.1 91.5 REMARK 620 7 HOH A1021 O 121.7 66.9 149.4 98.7 85.0 49.8 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 113 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A1007 O REMARK 620 2 HOH A1008 O 91.1 REMARK 620 3 HOH A1009 O 94.5 87.9 REMARK 620 4 2DA B 112 OP2 160.0 100.6 102.0 REMARK 620 5 HOH B 531 O 82.7 88.0 175.0 81.6 REMARK 620 6 HOH B 538 O 86.0 175.9 95.3 81.3 88.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 1 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 501 O REMARK 620 2 HOH B 502 O 92.2 REMARK 620 3 HOH B 503 O 176.5 89.2 REMARK 620 4 HOH B 504 O 92.7 93.1 84.1 REMARK 620 5 HOH B 505 O 89.5 174.2 88.8 81.3 REMARK 620 6 HOH C 543 O 89.4 93.1 93.7 173.4 92.5 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 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 833 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 834 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DDS A 835 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 113 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3LWM RELATED DB: PDB REMARK 900 RELATED ID: 3LWL RELATED DB: PDB REMARK 900 RELATED ID: 3PO5 RELATED DB: PDB DBREF 3PO4 A 293 832 UNP P19821 DPO1_THEAQ 293 832 DBREF 3PO4 B 101 112 PDB 3PO4 3PO4 101 112 DBREF 3PO4 C 205 216 PDB 3PO4 3PO4 205 216 SEQADV 3PO4 LYS A 614 UNP P19821 ILE 614 ENGINEERED MUTATION SEQADV 3PO4 LYS A 747 UNP P19821 MET 747 ENGINEERED MUTATION 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 LYS 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 LYS 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 2DA SEQRES 1 C 12 DT DG DC DG DC DC DG DT DG DG DT DC MODRES 3PO4 2DA B 112 DA 2',3'-DIDEOXYADENOSINE-5'-MONOPHOSPHATE HET 2DA B 112 20 HET MG A 1 1 HET NA A 833 1 HET GOL A 834 6 HET DDS A 835 29 HET MG B 1 1 HET MG B 113 1 HETNAM 2DA 2',3'-DIDEOXYADENOSINE-5'-MONOPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETNAM GOL GLYCEROL HETNAM DDS 2',3'-DIDEOXYADENOSINE TRIPHOSPHATE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 2DA C10 H14 N5 O5 P FORMUL 4 MG 3(MG 2+) FORMUL 5 NA NA 1+ FORMUL 6 GOL C3 H8 O3 FORMUL 7 DDS C10 H16 N5 O11 P3 FORMUL 10 HOH *548(H2 O) HELIX 1 1 GLU A 337 ARG A 343 1 7 HELIX 2 2 LEU A 352 GLU A 363 1 12 HELIX 3 3 ASP A 372 ASP A 381 1 10 HELIX 4 4 THR A 386 GLY A 395 1 10 HELIX 5 5 GLU A 401 LEU A 420 1 20 HELIX 6 6 GLU A 423 VAL A 433 1 11 HELIX 7 7 VAL A 433 GLY A 448 1 16 HELIX 8 8 ASP A 452 GLY A 479 1 28 HELIX 9 9 SER A 486 ASP A 496 1 11 HELIX 10 10 SER A 515 ALA A 521 1 7 HELIX 11 11 HIS A 526 TYR A 545 1 20 HELIX 12 12 PRO A 548 ILE A 553 5 6 HELIX 13 13 THR A 588 ARG A 593 1 6 HELIX 14 14 ILE A 594 ARG A 596 5 3 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 PHE A 647 1 11 HELIX 18 18 PRO A 650 VAL A 654 5 5 HELIX 19 19 ASP A 655 GLY A 672 1 18 HELIX 20 20 SER A 674 ALA A 683 1 10 HELIX 21 21 PRO A 685 PHE A 700 1 16 HELIX 22 22 PHE A 700 GLY A 718 1 19 HELIX 23 23 VAL A 737 MET A 775 1 39 HELIX 24 24 ARG A 795 GLY A 809 1 15 HELIX 25 25 ASP A 826 LYS A 831 1 6 SHEET 1 A 3 PHE A 306 LEU A 311 0 SHEET 2 A 3 LEU A 321 ARG A 328 -1 O ALA A 327 N PHE A 306 SHEET 3 A 3 ARG A 331 ARG A 334 -1 O HIS A 333 N ALA A 326 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 GLY A 824 N LEU A 606 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 2DA B 112 1555 1555 1.58 LINK MG MG A 1 O HOH A 19 1555 1555 2.09 LINK MG MG A 1 O2A DDS A 835 1555 1555 1.99 LINK MG MG A 1 O2B DDS A 835 1555 1555 2.05 LINK MG MG A 1 O3G DDS A 835 1555 1555 2.10 LINK MG MG A 1 O HOH A 842 1555 1555 2.06 LINK MG MG A 1 O HOH A 851 1555 1555 2.07 LINK MG MG A 1 O HOH A1021 1555 1555 2.11 LINK OE2 GLU A 507 NA NA A 833 1555 1555 2.47 LINK O HOH A1007 MG MG B 113 1555 1555 2.08 LINK O HOH A1008 MG MG B 113 1555 1555 2.12 LINK O HOH A1009 MG MG B 113 1555 1555 2.04 LINK MG MG B 1 O HOH B 501 1555 1555 2.06 LINK MG MG B 1 O HOH B 502 1555 1555 2.09 LINK MG MG B 1 O HOH B 503 1555 1555 2.09 LINK MG MG B 1 O HOH B 504 1555 1555 2.10 LINK MG MG B 1 O HOH B 505 1555 1555 2.10 LINK MG MG B 1 O HOH C 543 1555 1555 2.07 LINK OP2 2DA B 112 MG MG B 113 1555 1555 2.28 LINK MG MG B 113 O HOH B 531 1555 1555 2.10 LINK MG MG B 113 O HOH B 538 1555 1555 2.06 CISPEP 1 TRP A 299 PRO A 300 0 3.22 CISPEP 2 ASP A 578 PRO A 579 0 -0.54 CISPEP 3 VAL A 649 PRO A 650 0 -9.68 SITE 1 AC1 5 HOH A 19 DDS A 835 HOH A 842 HOH A 851 SITE 2 AC1 5 HOH A1021 SITE 1 AC2 6 HOH A 278 GLU A 507 VAL A 737 LYS A 738 SITE 2 AC2 6 SER A 739 HOH A 958 SITE 1 AC3 4 HOH A 92 HOH A 141 TRP A 428 HOH A 972 SITE 1 AC4 18 MG A 1 HOH A 19 HOH A 249 HOH A 250 SITE 2 AC4 18 ARG A 587 GLN A 613 HIS A 639 ARG A 659 SITE 3 AC4 18 LYS A 663 PHE A 667 TYR A 671 ASP A 785 SITE 4 AC4 18 HOH A 842 HOH A 851 HOH A1009 HOH A1021 SITE 5 AC4 18 HOH B 81 2DA B 112 SITE 1 AC5 6 HOH B 501 HOH B 502 HOH B 503 HOH B 504 SITE 2 AC5 6 HOH B 505 HOH C 543 SITE 1 AC6 6 HOH A1007 HOH A1008 HOH A1009 2DA B 112 SITE 2 AC6 6 HOH B 531 HOH B 538 CRYST1 113.525 113.525 91.238 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 0.008809 0.005086 0.000000 0.00000 SCALE2 0.000000 0.010171 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010960 0.00000