HEADER TRANSFERASE 10-MAR-21 7M0B TITLE PRE-CATALYTIC QUATERNARY COMPLEX OF DNA POLYMERASE LAMBDA WITH BOUND TITLE 2 MISMATCHED DSB AND INCOMING DUMPNPP 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 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(*CP*GP*GP*CP*AP*G)-3'); COMPND 10 CHAIN: T; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'-D(*CP*AP*GP*TP*GP*C)-3'); COMPND 14 CHAIN: P; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 4; COMPND 17 MOLECULE: DNA (5'-D(P*GP*CP*CP*G)-3'); COMPND 18 CHAIN: D; COMPND 19 ENGINEERED: YES; COMPND 20 MOL_ID: 5; COMPND 21 MOLECULE: DNA (5'-D(*TP*AP*CP*TP*G)-3'); COMPND 22 CHAIN: U; COMPND 23 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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEXM; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630; SOURCE 14 MOL_ID: 3; SOURCE 15 SYNTHETIC: YES; SOURCE 16 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 17 ORGANISM_TAXID: 32630; SOURCE 18 MOL_ID: 4; SOURCE 19 SYNTHETIC: YES; SOURCE 20 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 21 ORGANISM_TAXID: 32630; SOURCE 22 MOL_ID: 5; SOURCE 23 SYNTHETIC: YES; SOURCE 24 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 25 ORGANISM_TAXID: 32630 KEYWDS NONHOMOLOGOUS END-JOINING, BASE EXCISION REPAIR, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.M.KAMINSKI,K.BEBENEK,L.C.PEDERSEN,T.A.KUNKEL REVDAT 3 25-OCT-23 7M0B 1 REMARK REVDAT 2 15-FEB-23 7M0B 1 JRNL REVDAT 1 16-MAR-22 7M0B 0 JRNL AUTH A.M.KAMINSKI,K.K.CHIRUVELLA,D.A.RAMSDEN,K.BEBENEK, JRNL AUTH 2 T.A.KUNKEL,L.C.PEDERSEN JRNL TITL ANALYSIS OF DIVERSE DOUBLE-STRAND BREAK SYNAPSIS WITH POL JRNL TITL 2 LAMBDA REVEALS BASIS FOR UNIQUE SUBSTRATE SPECIFICITY IN JRNL TITL 3 NONHOMOLOGOUS END-JOINING. JRNL REF NAT COMMUN V. 13 3806 2022 JRNL REFN ESSN 2041-1723 JRNL PMID 35778389 JRNL DOI 10.1038/S41467-022-31278-4 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19_4092 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.40 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 32401 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1621 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 39.4000 - 4.5700 0.97 2701 143 0.1721 0.1905 REMARK 3 2 4.5700 - 3.6300 0.99 2654 135 0.1409 0.1412 REMARK 3 3 3.6300 - 3.1700 1.00 2586 140 0.1589 0.1884 REMARK 3 4 3.1700 - 2.8800 1.00 2604 133 0.1689 0.2133 REMARK 3 5 2.8800 - 2.6800 0.97 2510 125 0.1720 0.1914 REMARK 3 6 2.6800 - 2.5200 1.00 2573 145 0.1802 0.2118 REMARK 3 7 2.5200 - 2.3900 1.00 2554 131 0.1773 0.2237 REMARK 3 8 2.3900 - 2.2900 1.00 2557 133 0.1800 0.2151 REMARK 3 9 2.2900 - 2.2000 1.00 2581 132 0.1867 0.2353 REMARK 3 10 2.2000 - 2.1200 1.00 2536 140 0.1938 0.2422 REMARK 3 11 2.1200 - 2.0600 1.00 2519 145 0.1984 0.3092 REMARK 3 12 2.0600 - 2.0000 0.94 2405 119 0.2245 0.2777 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) : 0.201 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.873 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.95 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.95 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 : 0.008 3173 REMARK 3 ANGLE : 0.938 4393 REMARK 3 CHIRALITY : 0.053 486 REMARK 3 PLANARITY : 0.005 487 REMARK 3 DIHEDRAL : 12.993 971 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A AND RESID 236:329 REMARK 3 ORIGIN FOR THE GROUP (A): -7.8004 25.5989 -26.4141 REMARK 3 T TENSOR REMARK 3 T11: 0.2410 T22: 0.1495 REMARK 3 T33: 0.1458 T12: -0.0108 REMARK 3 T13: 0.0767 T23: 0.0056 REMARK 3 L TENSOR REMARK 3 L11: 0.3960 L22: 1.0872 REMARK 3 L33: 0.5779 L12: -0.3664 REMARK 3 L13: -0.0782 L23: -0.2393 REMARK 3 S TENSOR REMARK 3 S11: 0.0827 S12: 0.0433 S13: 0.0297 REMARK 3 S21: -0.3178 S22: 0.0195 S23: -0.1640 REMARK 3 S31: -0.1562 S32: -0.0389 S33: 0.0264 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND RESID 330:386 REMARK 3 ORIGIN FOR THE GROUP (A): -13.5535 20.1886 0.9095 REMARK 3 T TENSOR REMARK 3 T11: 0.0822 T22: 0.1153 REMARK 3 T33: 0.0966 T12: 0.0179 REMARK 3 T13: -0.0071 T23: -0.0226 REMARK 3 L TENSOR REMARK 3 L11: 0.2626 L22: 0.6075 REMARK 3 L33: 0.4254 L12: 0.2311 REMARK 3 L13: -0.1097 L23: -0.0983 REMARK 3 S TENSOR REMARK 3 S11: -0.0711 S12: -0.1049 S13: 0.0047 REMARK 3 S21: 0.1464 S22: 0.1103 S23: -0.0951 REMARK 3 S31: -0.0190 S32: -0.1017 S33: 0.0038 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND RESID 387:495 REMARK 3 ORIGIN FOR THE GROUP (A): -11.9640 -5.3905 -7.2671 REMARK 3 T TENSOR REMARK 3 T11: 0.0937 T22: 0.0928 REMARK 3 T33: 0.1437 T12: -0.0137 REMARK 3 T13: -0.0103 T23: -0.0060 REMARK 3 L TENSOR REMARK 3 L11: 0.4191 L22: 1.1455 REMARK 3 L33: 1.0125 L12: 0.0340 REMARK 3 L13: 0.3091 L23: 0.0570 REMARK 3 S TENSOR REMARK 3 S11: 0.0386 S12: -0.0395 S13: -0.0419 REMARK 3 S21: 0.0234 S22: 0.0208 S23: 0.0507 REMARK 3 S31: 0.1017 S32: -0.0008 S33: 0.0197 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN A AND RESID 496:575 REMARK 3 ORIGIN FOR THE GROUP (A): -19.8909 1.7731 -27.6250 REMARK 3 T TENSOR REMARK 3 T11: 0.1820 T22: 0.1394 REMARK 3 T33: 0.1088 T12: -0.0076 REMARK 3 T13: -0.0215 T23: -0.0320 REMARK 3 L TENSOR REMARK 3 L11: 0.4235 L22: 0.2497 REMARK 3 L33: 0.5845 L12: -0.0961 REMARK 3 L13: 0.2431 L23: 0.2283 REMARK 3 S TENSOR REMARK 3 S11: -0.0262 S12: 0.0999 S13: -0.0379 REMARK 3 S21: -0.2124 S22: 0.0563 S23: -0.0062 REMARK 3 S31: -0.0045 S32: -0.0354 S33: 0.0154 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN T OR CHAIN D REMARK 3 ORIGIN FOR THE GROUP (A): -24.1498 21.6917 -26.8450 REMARK 3 T TENSOR REMARK 3 T11: 0.1986 T22: 0.2321 REMARK 3 T33: 0.0821 T12: 0.0725 REMARK 3 T13: -0.0482 T23: 0.0795 REMARK 3 L TENSOR REMARK 3 L11: 0.2341 L22: 0.2286 REMARK 3 L33: 0.2087 L12: -0.1412 REMARK 3 L13: -0.1143 L23: 0.1816 REMARK 3 S TENSOR REMARK 3 S11: -0.0743 S12: 0.4045 S13: -0.1677 REMARK 3 S21: -0.1840 S22: 0.3901 S23: 0.0120 REMARK 3 S31: -0.1602 S32: -0.3347 S33: 0.0667 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN U OR CHAIN P REMARK 3 ORIGIN FOR THE GROUP (A): -25.2750 10.2653 -7.9376 REMARK 3 T TENSOR REMARK 3 T11: 0.0965 T22: 0.1637 REMARK 3 T33: 0.1367 T12: -0.0264 REMARK 3 T13: 0.0363 T23: -0.0169 REMARK 3 L TENSOR REMARK 3 L11: 0.0856 L22: 0.2668 REMARK 3 L33: 0.1643 L12: -0.1652 REMARK 3 L13: 0.0684 L23: -0.0483 REMARK 3 S TENSOR REMARK 3 S11: -0.1350 S12: 0.0797 S13: 0.0241 REMARK 3 S21: 0.0695 S22: 0.1318 S23: 0.0049 REMARK 3 S31: 0.1844 S32: -0.1883 S33: 0.0038 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 7M0B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-MAR-21. REMARK 100 THE DEPOSITION ID IS D_1000255338. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-NOV-20 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 6.5 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 : DOUBLE CRYSTAL SI(III) 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 : 32471 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 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 (%) : 99.2 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.15300 REMARK 200 FOR THE DATA SET : 13.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.81900 REMARK 200 FOR SHELL : 1.550 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: 2PFO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 76.5MM NA CACODYLATE PH 6.5, 0.153M REMARK 280 AMMONIUM SULFATE, 22.95% (W/V) PEG8000, 13.5% (V/V) GLYCEROL, REMARK 280 0.2M NDSB-201, VAPOR DIFFUSION, 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 28.18400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 69.70300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.98050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 69.70300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.18400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.98050 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: PENTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: PENTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6820 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -118.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, T, P, D, U 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 GLY A 230 REMARK 465 SER A 231 REMARK 465 ALA A 232 REMARK 465 ALA A 233 REMARK 465 ALA A 234 REMARK 465 VAL A 235 REMARK 465 ARG A 538 REMARK 465 ASN A 539 REMARK 465 THR A 540 REMARK 465 HIS A 541 REMARK 465 GLY A 542 REMARK 465 CYS A 543 REMARK 465 LYS A 544 REMARK 465 VAL A 545 REMARK 465 GLY A 546 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 ASP A 237 CG OD1 OD2 REMARK 470 LYS A 238 CE NZ REMARK 470 LEU A 254 CD1 CD2 REMARK 470 HIS A 255 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 265 CD CE NZ REMARK 470 GLN A 297 CG CD OE1 NE2 REMARK 470 LYS A 307 CG CD CE NZ REMARK 470 ARG A 308 CD NE CZ NH1 NH2 REMARK 470 LEU A 317 CD1 CD2 REMARK 470 ARG A 323 NE CZ NH1 NH2 REMARK 470 LYS A 324 CE NZ REMARK 470 GLU A 385 OE1 OE2 REMARK 470 GLU A 390 CD OE1 OE2 REMARK 470 LEU A 411 CD1 CD2 REMARK 470 ARG A 438 CZ NH1 NH2 REMARK 470 ARG A 441 CD NE CZ NH1 NH2 REMARK 470 GLN A 453 CG CD OE1 NE2 REMARK 470 GLU A 466 CG CD OE1 OE2 REMARK 470 ASN A 467 CG OD1 ND2 REMARK 470 GLN A 469 CG CD OE1 NE2 REMARK 470 LYS A 523 NZ REMARK 470 LYS A 557 CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O2 DC T 1 O HOH T 101 2.14 REMARK 500 O HOH A 1027 O HOH A 1052 2.18 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 DG D 1 P DG D 1 OP3 -0.121 REMARK 500 DC D 3 O3' DC D 3 C3' -0.039 REMARK 500 DC U 3 O3' DC U 3 C3' -0.050 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 D 2 O4' - C1' - N1 ANGL. DEV. = 2.5 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 THR A 250 62.68 -116.92 REMARK 500 CYS A 415 -138.57 -111.81 REMARK 500 ASP A 459 146.22 -170.59 REMARK 500 SER A 463 94.59 -162.70 REMARK 500 ASP A 574 59.21 -93.39 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 A1098 DISTANCE = 6.00 ANGSTROMS REMARK 525 HOH A1099 DISTANCE = 6.15 ANGSTROMS 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 705 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 300 O REMARK 620 2 ILE A 302 O 95.3 REMARK 620 3 ILE A 305 O 93.5 77.9 REMARK 620 4 HOH A 931 O 86.0 80.5 158.3 REMARK 620 5 DC D 3 OP1 177.9 83.6 88.0 92.0 REMARK 620 6 HOH D 117 O 103.4 157.3 113.2 87.9 77.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 704 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 339 O REMARK 620 2 ILE A 341 O 104.8 REMARK 620 3 ALA A 344 O 89.5 86.3 REMARK 620 4 HOH A1028 O 87.6 94.3 177.1 REMARK 620 5 DG P 5 OP1 160.5 94.7 91.2 91.6 REMARK 620 6 HOH P 103 O 70.2 168.6 83.5 95.7 90.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 702 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 427 OD2 REMARK 620 2 ASP A 429 OD1 83.7 REMARK 620 3 ASP A 490 OD2 88.9 101.4 REMARK 620 4 DUP A 701 O2A 97.0 88.4 169.1 REMARK 620 5 HOH A 937 O 83.8 162.9 89.9 81.7 REMARK 620 6 DC P 6 O3' 160.4 98.9 71.5 102.5 96.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 703 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 427 OD1 REMARK 620 2 ASP A 429 OD2 88.6 REMARK 620 3 DUP A 701 O2A 96.1 91.9 REMARK 620 4 DUP A 701 O2B 171.5 96.1 90.8 REMARK 620 5 DUP A 701 O3G 89.6 176.6 91.2 85.3 REMARK 620 6 HOH A 913 O 83.0 86.3 178.0 90.2 90.6 REMARK 620 N 1 2 3 4 5 DBREF 7M0B A 234 575 UNP Q9UGP5 DPOLL_HUMAN 234 575 DBREF 7M0B T 1 6 PDB 7M0B 7M0B 1 6 DBREF 7M0B P 1 6 PDB 7M0B 7M0B 1 6 DBREF 7M0B D 1 4 PDB 7M0B 7M0B 1 4 DBREF 7M0B U 1 5 PDB 7M0B 7M0B 1 5 SEQADV 7M0B GLY A 230 UNP Q9UGP5 EXPRESSION TAG SEQADV 7M0B SER A 231 UNP Q9UGP5 EXPRESSION TAG SEQADV 7M0B ALA A 232 UNP Q9UGP5 EXPRESSION TAG SEQADV 7M0B ALA A 233 UNP Q9UGP5 EXPRESSION TAG SEQRES 1 A 346 GLY SER ALA ALA ALA VAL LEU ASP LYS TRP VAL CYS ALA SEQRES 2 A 346 GLN PRO SER SER GLN LYS ALA THR ASN HIS ASN LEU HIS SEQRES 3 A 346 ILE THR GLU LYS LEU GLU VAL LEU ALA LYS ALA TYR SER SEQRES 4 A 346 VAL GLN GLY ASP LYS TRP ARG ALA LEU GLY TYR ALA LYS SEQRES 5 A 346 ALA ILE ASN ALA LEU LYS SER PHE HIS LYS PRO VAL THR SEQRES 6 A 346 SER TYR GLN GLU ALA CYS SER ILE PRO GLY ILE GLY LYS SEQRES 7 A 346 ARG MET ALA GLU LYS ILE ILE GLU ILE LEU GLU SER GLY SEQRES 8 A 346 HIS LEU ARG LYS LEU ASP HIS ILE SER GLU SER VAL PRO SEQRES 9 A 346 VAL LEU GLU LEU PHE SER ASN ILE TRP GLY ALA GLY THR SEQRES 10 A 346 LYS THR ALA GLN MET TRP TYR GLN GLN GLY PHE ARG SER SEQRES 11 A 346 LEU GLU ASP ILE ARG SER GLN ALA SER LEU THR THR GLN SEQRES 12 A 346 GLN ALA ILE GLY LEU LYS HIS TYR SER ASP PHE LEU GLU SEQRES 13 A 346 ARG MET PRO ARG GLU GLU ALA THR GLU ILE GLU GLN THR SEQRES 14 A 346 VAL GLN LYS ALA ALA GLN ALA PHE ASN SER GLY LEU LEU SEQRES 15 A 346 CYS VAL ALA CYS GLY SER TYR ARG ARG GLY LYS ALA THR SEQRES 16 A 346 CYS GLY ASP VAL ASP VAL LEU ILE THR HIS PRO ASP GLY SEQRES 17 A 346 ARG SER HIS ARG GLY ILE PHE SER ARG LEU LEU ASP SER SEQRES 18 A 346 LEU ARG GLN GLU GLY PHE LEU THR ASP ASP LEU VAL SER SEQRES 19 A 346 GLN GLU GLU ASN GLY GLN GLN GLN LYS TYR LEU GLY VAL SEQRES 20 A 346 CYS ARG LEU PRO GLY PRO GLY ARG ARG HIS ARG ARG LEU SEQRES 21 A 346 ASP ILE ILE VAL VAL PRO TYR SER GLU PHE ALA CYS ALA SEQRES 22 A 346 LEU LEU TYR PHE THR GLY SER ALA HIS PHE ASN ARG SER SEQRES 23 A 346 MET ARG ALA LEU ALA LYS THR LYS GLY MET SER LEU SER SEQRES 24 A 346 GLU HIS ALA LEU SER THR ALA VAL VAL ARG ASN THR HIS SEQRES 25 A 346 GLY CYS LYS VAL GLY PRO GLY ARG VAL LEU PRO THR PRO SEQRES 26 A 346 THR GLU LYS ASP VAL PHE ARG LEU LEU GLY LEU PRO TYR SEQRES 27 A 346 ARG GLU PRO ALA GLU ARG ASP TRP SEQRES 1 T 6 DC DG DG DC DA DG SEQRES 1 P 6 DC DA DG DT DG DC SEQRES 1 D 4 DG DC DC DG SEQRES 1 U 5 DT DA DC DT DG HET DUP A 701 28 HET MG A 702 1 HET MG A 703 1 HET NA A 704 1 HET NA A 705 1 HET CL A 706 1 HET CL A 707 1 HET CL A 708 1 HET CL A 709 1 HET SO4 A 710 5 HET SO4 A 711 5 HET EDO A 712 4 HETNAM DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETNAM SO4 SULFATE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 6 DUP C9 H16 N3 O13 P3 FORMUL 7 MG 2(MG 2+) FORMUL 9 NA 2(NA 1+) FORMUL 11 CL 4(CL 1-) FORMUL 15 SO4 2(O4 S 2-) FORMUL 17 EDO C2 H6 O2 FORMUL 18 HOH *379(H2 O) HELIX 1 AA1 TRP A 239 GLN A 243 5 5 HELIX 2 AA2 PRO A 244 ASN A 251 5 8 HELIX 3 AA3 ASN A 253 GLY A 271 1 19 HELIX 4 AA4 ASP A 272 PHE A 289 1 18 HELIX 5 AA5 SER A 295 ILE A 302 1 8 HELIX 6 AA6 GLY A 306 GLY A 320 1 15 HELIX 7 AA7 LEU A 322 ILE A 328 5 7 HELIX 8 AA8 SER A 331 ASN A 340 1 10 HELIX 9 AA9 GLY A 345 GLN A 355 1 11 HELIX 10 AB1 SER A 359 ALA A 367 1 9 HELIX 11 AB2 THR A 370 HIS A 379 1 10 HELIX 12 AB3 HIS A 379 GLU A 385 1 7 HELIX 13 AB4 ARG A 389 ASN A 407 1 19 HELIX 14 AB5 CYS A 415 ARG A 420 1 6 HELIX 15 AB6 ILE A 443 GLU A 454 1 12 HELIX 16 AB7 PRO A 495 SER A 497 5 3 HELIX 17 AB8 GLU A 498 GLY A 508 1 11 HELIX 18 AB9 SER A 509 LYS A 523 1 15 HELIX 19 AC1 THR A 555 LEU A 563 1 9 HELIX 20 AC2 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 ASP A 427 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 430 SHEET 4 AA2 5 LYS A 472 CYS A 477 -1 N GLY A 475 O LEU A 489 SHEET 5 AA2 5 LEU A 457 SER A 463 -1 N THR A 458 O VAL A 476 SHEET 1 AA3 2 MET A 525 LEU A 527 0 SHEET 2 AA3 2 LEU A 532 THR A 534 -1 O SER A 533 N SER A 526 LINK O CYS A 300 NA NA A 705 1555 1555 2.36 LINK O ILE A 302 NA NA A 705 1555 1555 2.77 LINK O ILE A 305 NA NA A 705 1555 1555 2.34 LINK O SER A 339 NA NA A 704 1555 1555 2.30 LINK O ILE A 341 NA NA A 704 1555 1555 2.40 LINK O ALA A 344 NA NA A 704 1555 1555 2.30 LINK OD2 ASP A 427 MG A MG A 702 1555 1555 1.99 LINK OD1 ASP A 427 MG MG A 703 1555 1555 2.06 LINK OD1 ASP A 429 MG A MG A 702 1555 1555 2.20 LINK OD2 ASP A 429 MG MG A 703 1555 1555 2.09 LINK OD2 ASP A 490 MG A MG A 702 1555 1555 2.21 LINK O2A DUP A 701 MG A MG A 702 1555 1555 2.34 LINK O2A DUP A 701 MG MG A 703 1555 1555 2.08 LINK O2B DUP A 701 MG MG A 703 1555 1555 2.01 LINK O3G DUP A 701 MG MG A 703 1555 1555 2.02 LINK MG A MG A 702 O HOH A 937 1555 1555 2.34 LINK MG A MG A 702 O3'A DC P 6 1555 1555 2.27 LINK MG MG A 703 O HOH A 913 1555 1555 2.15 LINK NA NA A 704 O HOH A1028 1555 1555 2.38 LINK NA NA A 704 OP1 DG P 5 1555 1555 2.32 LINK NA NA A 704 O HOH P 103 1555 1555 2.82 LINK NA NA A 705 O HOH A 931 1555 1555 2.49 LINK NA NA A 705 OP1 DC D 3 1555 1555 3.12 LINK NA NA A 705 O HOH D 117 1555 1555 2.44 CISPEP 1 GLY A 508 SER A 509 0 1.33 CRYST1 56.368 59.961 139.406 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 0.017741 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016678 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007173 0.00000