HEADER REPLICATION 21-MAR-21 7M4L TITLE DNA POLYMERASE LAMBDA, TTPAS:AT MN2+ PRODUCT STATE TERNARY COMPLEX, 60 TITLE 2 MIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE LAMBDA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: POL LAMBDA,DNA POLYMERASE BETA-2,POL BETA2,DNA POLYMERASE COMPND 5 KAPPA; COMPND 6 EC: 2.7.7.7,4.2.99.-; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: DNA (5'-D(*CP*GP*GP*CP*AP*GP*TP*AP*CP*TP*G)-3'); COMPND 11 CHAIN: T; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: DNA (5'-D(*CP*AP*GP*TP*AP*CP*(YQS))-3'); COMPND 15 CHAIN: P; COMPND 16 ENGINEERED: YES; COMPND 17 MOL_ID: 4; COMPND 18 MOLECULE: DNA (5'-D(P*GP*CP*CP*G)-3'); COMPND 19 CHAIN: D; COMPND 20 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: POLL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_COMMON: HUMAN; SOURCE 15 ORGANISM_TAXID: 9606; SOURCE 16 MOL_ID: 3; SOURCE 17 SYNTHETIC: YES; SOURCE 18 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 19 ORGANISM_COMMON: HUMAN; SOURCE 20 ORGANISM_TAXID: 9606; SOURCE 21 MOL_ID: 4; SOURCE 22 SYNTHETIC: YES; SOURCE 23 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 24 ORGANISM_COMMON: HUMAN; SOURCE 25 ORGANISM_TAXID: 9606 KEYWDS TIME-LAPSE CRYSTALLOGRAPHY, DOUBLE STRAND BREAK REPAIR, DNA SYNTHESIS KEYWDS 2 FIDELITY, REPLICATION EXPDTA X-RAY DIFFRACTION AUTHOR J.A.JAMSEN,S.H.WILSON REVDAT 2 18-OCT-23 7M4L 1 REMARK REVDAT 1 06-JUL-22 7M4L 0 JRNL AUTH J.A.JAMSEN,D.D.SHOCK,S.H.WILSON JRNL TITL WATCHING RIGHT AND WRONG NUCLEOTIDE INSERTION CAPTURES JRNL TITL 2 HIDDEN POLYMERASE FIDELITY CHECKPOINTS. JRNL REF NAT COMMUN V. 13 3193 2022 JRNL REFN ESSN 2041-1723 JRNL PMID 35680862 JRNL DOI 10.1038/S41467-022-30141-W REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.2-3472 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.03 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 53481 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.910 REMARK 3 FREE R VALUE TEST SET COUNT : 2626 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 40.0290 - 4.5373 0.99 2943 150 0.1986 0.2118 REMARK 3 2 4.5373 - 3.6021 1.00 2825 155 0.1560 0.1964 REMARK 3 3 3.6021 - 3.1470 1.00 2786 135 0.1757 0.1904 REMARK 3 4 3.1470 - 2.8593 1.00 2789 144 0.1941 0.1978 REMARK 3 5 2.8593 - 2.6544 1.00 2764 142 0.1948 0.2245 REMARK 3 6 2.6544 - 2.4980 1.00 2751 145 0.1910 0.2136 REMARK 3 7 2.4980 - 2.3729 1.00 2763 140 0.1825 0.2133 REMARK 3 8 2.3729 - 2.2696 1.00 2741 144 0.1870 0.2290 REMARK 3 9 2.2696 - 2.1822 1.00 2731 141 0.1847 0.2239 REMARK 3 10 2.1822 - 2.1069 1.00 2723 138 0.1952 0.2231 REMARK 3 11 2.1069 - 2.0411 1.00 2735 140 0.2045 0.2288 REMARK 3 12 2.0411 - 1.9827 1.00 2735 145 0.2091 0.2896 REMARK 3 13 1.9827 - 1.9305 1.00 2725 141 0.2182 0.2494 REMARK 3 14 1.9305 - 1.8834 0.99 2694 139 0.2429 0.3070 REMARK 3 15 1.8834 - 1.8406 0.98 2661 137 0.2526 0.2873 REMARK 3 16 1.8406 - 1.8014 0.94 2558 130 0.2555 0.2849 REMARK 3 17 1.8014 - 1.7654 0.89 2411 125 0.2614 0.2884 REMARK 3 18 1.7654 - 1.7321 0.86 2347 121 0.2722 0.2969 REMARK 3 19 1.7321 - 1.7012 0.81 2173 114 0.2891 0.3014 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.820 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.69 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 251:322 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.183 -29.863 25.310 REMARK 3 T TENSOR REMARK 3 T11: 0.5829 T22: 0.8571 REMARK 3 T33: 0.6412 T12: 0.1616 REMARK 3 T13: -0.0931 T23: 0.1619 REMARK 3 L TENSOR REMARK 3 L11: 0.6461 L22: 1.4642 REMARK 3 L33: 1.0608 L12: -0.4971 REMARK 3 L13: -0.4415 L23: 0.0110 REMARK 3 S TENSOR REMARK 3 S11: -0.2094 S12: -0.8318 S13: -0.0864 REMARK 3 S21: 0.4415 S22: 0.0594 S23: -0.5398 REMARK 3 S31: 0.5787 S32: 0.6422 S33: -0.0035 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN A AND RESID 323:471 ) REMARK 3 ORIGIN FOR THE GROUP (A): -12.247 -7.850 5.220 REMARK 3 T TENSOR REMARK 3 T11: 0.2420 T22: 0.2626 REMARK 3 T33: 0.2496 T12: 0.0272 REMARK 3 T13: -0.0187 T23: -0.0233 REMARK 3 L TENSOR REMARK 3 L11: 3.1314 L22: 1.5782 REMARK 3 L33: 1.8794 L12: 0.2702 REMARK 3 L13: -0.9447 L23: 0.6553 REMARK 3 S TENSOR REMARK 3 S11: 0.0909 S12: -0.0146 S13: 0.3265 REMARK 3 S21: -0.0564 S22: 0.0704 S23: -0.1139 REMARK 3 S31: -0.1908 S32: 0.0218 S33: 0.0270 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: ( CHAIN A AND RESID 472:575 ) REMARK 3 ORIGIN FOR THE GROUP (A): -18.767 -4.041 23.189 REMARK 3 T TENSOR REMARK 3 T11: 0.3924 T22: 0.5187 REMARK 3 T33: 0.3601 T12: -0.0305 REMARK 3 T13: -0.0228 T23: -0.1508 REMARK 3 L TENSOR REMARK 3 L11: 2.2362 L22: 1.1055 REMARK 3 L33: 2.4052 L12: -0.5349 REMARK 3 L13: -1.1226 L23: 0.0478 REMARK 3 S TENSOR REMARK 3 S11: 0.0910 S12: -0.7872 S13: 0.1758 REMARK 3 S21: 0.3602 S22: 0.0321 S23: 0.0453 REMARK 3 S31: -0.0408 S32: 0.2021 S33: 0.0285 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: ( CHAIN T AND RESID 1:4 ) REMARK 3 ORIGIN FOR THE GROUP (A): -27.869 -26.100 26.808 REMARK 3 T TENSOR REMARK 3 T11: 0.5530 T22: 0.6606 REMARK 3 T33: 0.4371 T12: -0.0175 REMARK 3 T13: -0.0068 T23: 0.2147 REMARK 3 L TENSOR REMARK 3 L11: 0.1546 L22: 0.1039 REMARK 3 L33: 0.0458 L12: 0.1231 REMARK 3 L13: 0.0607 L23: 0.0357 REMARK 3 S TENSOR REMARK 3 S11: 0.1008 S12: -0.4714 S13: 0.3468 REMARK 3 S21: -0.0688 S22: 0.1243 S23: 0.7988 REMARK 3 S31: 0.1072 S32: -0.3444 S33: 0.0008 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: ( CHAIN T AND RESID 5:11 ) REMARK 3 ORIGIN FOR THE GROUP (A): -26.682 -9.319 9.896 REMARK 3 T TENSOR REMARK 3 T11: 0.3498 T22: 0.3119 REMARK 3 T33: 0.3360 T12: -0.0037 REMARK 3 T13: -0.0106 T23: -0.0205 REMARK 3 L TENSOR REMARK 3 L11: 0.2896 L22: 0.6335 REMARK 3 L33: 0.2016 L12: 0.3178 REMARK 3 L13: 0.0212 L23: 0.2642 REMARK 3 S TENSOR REMARK 3 S11: 0.1649 S12: -0.1380 S13: 0.1068 REMARK 3 S21: 0.0157 S22: -0.0176 S23: 0.0670 REMARK 3 S31: -0.1316 S32: 0.2003 S33: 0.0001 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: ( CHAIN P AND ( RESID 1:6 OR RESID 7:7 ) ) REMARK 3 ORIGIN FOR THE GROUP (A): -23.232 -14.133 9.802 REMARK 3 T TENSOR REMARK 3 T11: 0.3144 T22: 0.3204 REMARK 3 T33: 0.2798 T12: -0.0022 REMARK 3 T13: -0.0166 T23: -0.0699 REMARK 3 L TENSOR REMARK 3 L11: 0.2092 L22: 0.2732 REMARK 3 L33: 0.2259 L12: -0.0620 REMARK 3 L13: -0.2145 L23: 0.0867 REMARK 3 S TENSOR REMARK 3 S11: 0.1476 S12: -0.5734 S13: 0.2005 REMARK 3 S21: 0.1145 S22: -0.1204 S23: -0.2259 REMARK 3 S31: -0.3401 S32: -0.1087 S33: -0.0002 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: ( CHAIN D AND RESID 1:4 ) REMARK 3 ORIGIN FOR THE GROUP (A): -19.323 -28.631 29.508 REMARK 3 T TENSOR REMARK 3 T11: 0.6304 T22: 0.5759 REMARK 3 T33: 0.3561 T12: 0.0145 REMARK 3 T13: 0.0257 T23: 0.1290 REMARK 3 L TENSOR REMARK 3 L11: 0.2839 L22: 0.2597 REMARK 3 L33: 0.3810 L12: 0.0610 REMARK 3 L13: -0.0208 L23: 0.1796 REMARK 3 S TENSOR REMARK 3 S11: 0.1950 S12: -0.4173 S13: -0.2067 REMARK 3 S21: 0.5409 S22: 0.2100 S23: 0.1603 REMARK 3 S31: 0.6567 S32: 0.2832 S33: 0.0079 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 7M4L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-MAR-21. REMARK 100 THE DEPOSITION ID IS D_1001310106. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-AUG-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 53587 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 82.6 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.71500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: HKL-3000 REMARK 200 STARTING MODEL: 3UPQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 80-95MM BICINE PH 8.3, 0.3M NA-K REMARK 280 TARTRATE, 18-22.5% POLYPURE PEG, PH 7.5, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 27.98500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 70.06500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.37650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 70.06500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.98500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.37650 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6260 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -62.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, T, P, D 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 242 REMARK 465 GLN A 243 REMARK 465 PRO A 244 REMARK 465 SER A 245 REMARK 465 SER A 246 REMARK 465 GLN A 247 REMARK 465 LYS A 248 REMARK 465 ALA A 249 REMARK 465 THR A 250 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 HIS A 252 CG ND1 CD2 CE1 NE2 REMARK 470 LEU A 254 CG CD1 CD2 REMARK 470 ILE A 256 CD1 REMARK 470 GLU A 258 CG CD OE1 OE2 REMARK 470 LYS A 259 CD CE NZ REMARK 470 GLU A 261 CD OE1 OE2 REMARK 470 LEU A 263 CD1 CD2 REMARK 470 LYS A 265 CD CE NZ REMARK 470 LYS A 273 CE NZ REMARK 470 ASN A 284 OD1 ND2 REMARK 470 LYS A 287 CG CD CE NZ REMARK 470 PHE A 289 CD1 CE1 CE2 CZ REMARK 470 LYS A 291 CE NZ REMARK 470 VAL A 293 CG1 CG2 REMARK 470 THR A 294 OG1 CG2 REMARK 470 GLN A 297 CG CD OE1 NE2 REMARK 470 SER A 301 OG REMARK 470 ILE A 305 CD1 REMARK 470 LYS A 307 CE NZ REMARK 470 ARG A 308 CZ NH1 NH2 REMARK 470 ILE A 313 CD1 REMARK 470 ILE A 314 CD1 REMARK 470 GLU A 318 CD OE1 OE2 REMARK 470 LEU A 322 CD1 CD2 REMARK 470 ARG A 323 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 324 CG CD CE NZ REMARK 470 ASP A 326 OD1 OD2 REMARK 470 GLU A 330 CG CD OE1 OE2 REMARK 470 GLN A 366 OE1 NE2 REMARK 470 LYS A 401 CG CD CE NZ REMARK 470 PHE A 406 CE1 CE2 CZ REMARK 470 LEU A 411 CD1 CD2 REMARK 470 LYS A 422 CD CE NZ REMARK 470 ARG A 438 CG CD NE CZ NH1 NH2 REMARK 470 SER A 439 OG REMARK 470 ARG A 441 CG CD NE CZ NH1 NH2 REMARK 470 ILE A 443 CD1 REMARK 470 SER A 445 OG REMARK 470 ARG A 446 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 449 OD1 OD2 REMARK 470 GLN A 453 CG CD OE1 NE2 REMARK 470 LYS A 463 NZ REMARK 470 GLU A 470 CD OE1 OE2 REMARK 470 ARG A 485 CD NE CZ NH1 NH2 REMARK 470 THR A 540 OG1 CG2 REMARK 470 LYS A 544 CG CD CE NZ REMARK 470 VAL A 545 CG1 CG2 REMARK 470 LYS A 557 CD CE NZ REMARK 470 LEU A 565 CD1 CD2 REMARK 470 ARG A 568 NH1 NH2 REMARK 470 GLU A 569 OE1 OE2 REMARK 470 GLU A 572 CG CD OE1 OE2 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 O21 PPV A 606 O HOH A 701 2.10 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 SER A 339 CB SER A 339 OG -0.084 REMARK 500 TYR A 380 CE1 TYR A 380 CZ -0.096 REMARK 500 GLU A 390 CD GLU A 390 OE2 0.083 REMARK 500 DG T 2 O3' DG T 2 C3' -0.047 REMARK 500 DG T 6 N7 DG T 6 C8 0.036 REMARK 500 DA P 5 P DA P 5 O5' -0.077 REMARK 500 DG D 1 P DG D 1 OP3 -0.147 REMARK 500 DC D 3 O3' DC D 3 C3' -0.046 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 ARG A 420 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 MET A 516 CG - SD - CE ANGL. DEV. = -12.1 DEGREES REMARK 500 DG T 2 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 DT T 7 N3 - C4 - O4 ANGL. DEV. = 4.4 DEGREES REMARK 500 DC T 9 O5' - P - OP2 ANGL. DEV. = -5.7 DEGREES REMARK 500 DG P 3 OP1 - P - OP2 ANGL. DEV. = 10.2 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 A 415 -139.03 -106.55 REMARK 500 ARG A 438 -37.62 -138.35 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 864 DISTANCE = 5.89 ANGSTROMS REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 EDO A 608 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 NA A 605 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 300 O REMARK 620 2 ILE A 302 O 95.2 REMARK 620 3 ILE A 305 O 88.9 84.5 REMARK 620 4 DC D 3 OP1 172.0 92.7 90.5 REMARK 620 5 HOH D 102 O 86.6 159.8 75.5 85.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 604 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 339 O REMARK 620 2 ILE A 341 O 97.3 REMARK 620 3 ALA A 344 O 87.0 84.9 REMARK 620 4 HOH A 825 O 89.0 99.3 174.5 REMARK 620 5 DA P 5 OP1 164.6 97.8 91.7 91.2 REMARK 620 6 HOH P 107 O 73.8 167.2 85.4 89.9 90.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 603 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 382 OD2 REMARK 620 2 HIS A 486 ND1 102.1 REMARK 620 3 HOH A 751 O 83.6 92.9 REMARK 620 4 HOH A 804 O 111.1 91.8 163.2 REMARK 620 5 HOH A 828 O 157.2 91.7 77.6 86.2 REMARK 620 6 HOH P 114 O 80.1 172.9 94.1 81.2 88.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 601 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 427 OD1 REMARK 620 2 ASP A 429 OD2 94.7 REMARK 620 3 PPV A 606 O21 154.1 88.6 REMARK 620 4 PPV A 606 O22 90.3 174.2 88.1 REMARK 620 5 HOH A 701 O 94.3 99.6 59.8 82.9 REMARK 620 6 YQS P 7 O1A 100.5 91.6 105.2 84.6 160.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 602 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 427 OD2 REMARK 620 2 ASP A 429 OD1 98.7 REMARK 620 3 ASP A 490 OD2 99.4 100.5 REMARK 620 4 HOH A 766 O 75.7 164.8 94.4 REMARK 620 5 YQS P 7 O1A 110.4 87.8 147.6 81.1 REMARK 620 N 1 2 3 4 DBREF 7M4L A 242 575 UNP Q9UGP5 DPOLL_HUMAN 242 575 DBREF 7M4L T 1 11 PDB 7M4L 7M4L 1 11 DBREF 7M4L P 1 7 PDB 7M4L 7M4L 1 7 DBREF 7M4L D 1 4 PDB 7M4L 7M4L 1 4 SEQADV 7M4L LYS A 463 UNP Q9UGP5 SER 463 CONFLICT SEQADV 7M4L GLY A 464 UNP Q9UGP5 GLN 464 CONFLICT SEQADV 7M4L THR A 471 UNP Q9UGP5 GLU 466 CONFLICT SEQADV 7M4L A UNP Q9UGP5 ASN 467 DELETION SEQADV 7M4L A UNP Q9UGP5 GLY 468 DELETION SEQADV 7M4L A UNP Q9UGP5 GLN 469 DELETION SEQADV 7M4L A UNP Q9UGP5 GLN 470 DELETION SEQADV 7M4L A UNP Q9UGP5 GLN 471 DELETION SEQADV 7M4L ALA A 543 UNP Q9UGP5 CYS 543 ENGINEERED MUTATION SEQRES 1 A 329 ALA GLN PRO SER SER GLN LYS ALA THR ASN HIS ASN LEU SEQRES 2 A 329 HIS ILE THR GLU LYS LEU GLU VAL LEU ALA LYS ALA TYR SEQRES 3 A 329 SER VAL GLN GLY ASP LYS TRP ARG ALA LEU GLY TYR ALA SEQRES 4 A 329 LYS ALA ILE ASN ALA LEU LYS SER PHE HIS LYS PRO VAL SEQRES 5 A 329 THR SER TYR GLN GLU ALA CYS SER ILE PRO GLY ILE GLY SEQRES 6 A 329 LYS ARG MET ALA GLU LYS ILE ILE GLU ILE LEU GLU SER SEQRES 7 A 329 GLY HIS LEU ARG LYS LEU ASP HIS ILE SER GLU SER VAL SEQRES 8 A 329 PRO VAL LEU GLU LEU PHE SER ASN ILE TRP GLY ALA GLY SEQRES 9 A 329 THR LYS THR ALA GLN MET TRP TYR GLN GLN GLY PHE ARG SEQRES 10 A 329 SER LEU GLU ASP ILE ARG SER GLN ALA SER LEU THR THR SEQRES 11 A 329 GLN GLN ALA ILE GLY LEU LYS HIS TYR SER ASP PHE LEU SEQRES 12 A 329 GLU ARG MET PRO ARG GLU GLU ALA THR GLU ILE GLU GLN SEQRES 13 A 329 THR VAL GLN LYS ALA ALA GLN ALA PHE ASN SER GLY LEU SEQRES 14 A 329 LEU CYS VAL ALA CYS GLY SER TYR ARG ARG GLY LYS ALA SEQRES 15 A 329 THR CYS GLY ASP VAL ASP VAL LEU ILE THR HIS PRO ASP SEQRES 16 A 329 GLY ARG SER HIS ARG GLY ILE PHE SER ARG LEU LEU ASP SEQRES 17 A 329 SER LEU ARG GLN GLU GLY PHE LEU THR ASP ASP LEU VAL SEQRES 18 A 329 LYS GLY GLU THR LYS TYR LEU GLY VAL CYS ARG LEU PRO SEQRES 19 A 329 GLY PRO GLY ARG ARG HIS ARG ARG LEU ASP ILE ILE VAL SEQRES 20 A 329 VAL PRO TYR SER GLU PHE ALA CYS ALA LEU LEU TYR PHE SEQRES 21 A 329 THR GLY SER ALA HIS PHE ASN ARG SER MET ARG ALA LEU SEQRES 22 A 329 ALA LYS THR LYS GLY MET SER LEU SER GLU HIS ALA LEU SEQRES 23 A 329 SER THR ALA VAL VAL ARG ASN THR HIS GLY ALA LYS VAL SEQRES 24 A 329 GLY PRO GLY ARG VAL LEU PRO THR PRO THR GLU LYS ASP SEQRES 25 A 329 VAL PHE ARG LEU LEU GLY LEU PRO TYR ARG GLU PRO ALA SEQRES 26 A 329 GLU ARG ASP TRP SEQRES 1 T 11 DC DG DG DC DA DG DT DA DC DT DG SEQRES 1 P 7 DC DA DG DT DA DC YQS SEQRES 1 D 4 DG DC DC DG HET YQS P 7 20 HET MN A 601 1 HET MN A 602 1 HET MN A 603 1 HET NA A 604 1 HET NA A 605 1 HET PPV A 606 9 HET EDO A 607 4 HET EDO A 608 3 HET EDO A 609 4 HET EDO A 610 4 HET EDO A 611 4 HETNAM YQS [[(2~{R},3~{S},5~{R})-5-[5-METHYL-2,4- HETNAM 2 YQS BIS(OXIDANYLIDENE)PYRIMIDIN-1-YL]-3-OXIDANYL-OXOLAN-2- HETNAM 3 YQS YL]METHOXY-SULFANYL-PHOSPHORYL] PHOSPHONO HYDROGEN HETNAM 4 YQS PHOSPHATE HETNAM MN MANGANESE (II) ION HETNAM NA SODIUM ION HETNAM PPV PYROPHOSPHATE HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 YQS C10 H17 N2 O13 P3 S FORMUL 5 MN 3(MN 2+) FORMUL 8 NA 2(NA 1+) FORMUL 10 PPV H4 O7 P2 FORMUL 11 EDO 5(C2 H6 O2) FORMUL 16 HOH *243(H2 O) HELIX 1 AA1 ASN A 253 GLN A 270 1 18 HELIX 2 AA2 ASP A 272 SER A 288 1 17 HELIX 3 AA3 SER A 295 ILE A 302 1 8 HELIX 4 AA4 GLY A 306 GLY A 320 1 15 HELIX 5 AA5 LEU A 322 ILE A 328 5 7 HELIX 6 AA6 SER A 331 ASN A 340 1 10 HELIX 7 AA7 GLY A 345 GLN A 355 1 11 HELIX 8 AA8 SER A 359 ALA A 367 1 9 HELIX 9 AA9 THR A 370 HIS A 379 1 10 HELIX 10 AB1 HIS A 379 LEU A 384 1 6 HELIX 11 AB2 ARG A 389 ASN A 407 1 19 HELIX 12 AB3 CYS A 415 ARG A 420 1 6 HELIX 13 AB4 ILE A 443 GLU A 454 1 12 HELIX 14 AB5 PRO A 495 SER A 497 5 3 HELIX 15 AB6 GLU A 498 GLY A 508 1 11 HELIX 16 AB7 SER A 509 LYS A 523 1 15 HELIX 17 AB8 THR A 555 LEU A 563 1 9 HELIX 18 AB9 GLU A 569 ASP A 574 5 6 SHEET 1 AA1 2 MET A 387 PRO A 388 0 SHEET 2 AA1 2 THR A 424 CYS A 425 -1 O CYS A 425 N MET A 387 SHEET 1 AA2 5 LEU A 411 ALA A 414 0 SHEET 2 AA2 5 VAL A 428 THR A 433 -1 O LEU A 431 N VAL A 413 SHEET 3 AA2 5 ARG A 487 VAL A 493 1 O ASP A 490 N VAL A 428 SHEET 4 AA2 5 LYS A 472 CYS A 477 -1 N TYR A 473 O ILE A 491 SHEET 5 AA2 5 LEU A 457 LYS A 463 -1 N LEU A 461 O LEU A 474 SHEET 1 AA3 3 MET A 525 LEU A 527 0 SHEET 2 AA3 3 LEU A 532 THR A 534 -1 O SER A 533 N SER A 526 SHEET 3 AA3 3 ARG A 549 LEU A 551 -1 O LEU A 551 N LEU A 532 SHEET 1 AA4 2 VAL A 537 ARG A 538 0 SHEET 2 AA4 2 LYS A 544 GLY A 546 -1 O VAL A 545 N VAL A 537 LINK O3' DC P 6 PA YQS P 7 1555 1555 1.62 LINK O CYS A 300 NA NA A 605 1555 1555 2.60 LINK O ILE A 302 NA NA A 605 1555 1555 2.29 LINK O ILE A 305 NA NA A 605 1555 1555 2.79 LINK O SER A 339 NA NA A 604 1555 1555 2.37 LINK O ILE A 341 NA NA A 604 1555 1555 2.44 LINK O ALA A 344 NA NA A 604 1555 1555 2.33 LINK OD2 ASP A 382 MN MN A 603 1555 1555 2.16 LINK OD1 ASP A 427 MN MN A 601 1555 1555 2.10 LINK OD2 ASP A 427 MN MN A 602 1555 1555 2.02 LINK OD2 ASP A 429 MN MN A 601 1555 1555 2.11 LINK OD1 ASP A 429 MN MN A 602 1555 1555 2.14 LINK ND1 HIS A 486 MN MN A 603 1555 1555 2.38 LINK OD2 ASP A 490 MN MN A 602 1555 1555 2.25 LINK MN MN A 601 O21 PPV A 606 1555 1555 2.14 LINK MN MN A 601 O22 PPV A 606 1555 1555 2.12 LINK MN MN A 601 O HOH A 701 1555 1555 2.06 LINK MN MN A 601 O1A YQS P 7 1555 1555 2.08 LINK MN MN A 602 O HOH A 766 1555 1555 2.46 LINK MN MN A 602 O1A YQS P 7 1555 1555 2.43 LINK MN MN A 603 O HOH A 751 1555 1555 2.56 LINK MN MN A 603 O HOH A 804 1555 1555 2.35 LINK MN MN A 603 O HOH A 828 1555 1555 2.39 LINK MN MN A 603 O HOH P 114 1555 4545 2.29 LINK NA NA A 604 O HOH A 825 1555 1555 2.43 LINK NA NA A 604 OP1 DA P 5 1555 1555 2.27 LINK NA NA A 604 O HOH P 107 1555 1555 2.69 LINK NA NA A 605 OP1 DC D 3 1555 1555 3.09 LINK NA NA A 605 O HOH D 102 1555 1555 2.16 CISPEP 1 GLY A 508 SER A 509 0 2.00 CRYST1 55.970 62.753 140.130 90.00 90.00 90.00 P 21 21 21 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 0.017867 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015935 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007136 0.00000