HEADER REPLICATION 21-MAR-21 7M4F TITLE DNA POLYMERASE LAMBDA, DCTP:AT MG2+ PRODUCT STATE TERNARY COMPLEX, 300 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*C)-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 7M4F 1 REMARK REVDAT 1 06-JUL-22 7M4F 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. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX V1.15.2-3472 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.13 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 36477 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.910 REMARK 3 FREE R VALUE TEST SET COUNT : 1790 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 36.1280 - 4.5761 0.98 2838 144 0.2065 0.2206 REMARK 3 2 4.5761 - 3.6332 1.00 2751 151 0.1769 0.1985 REMARK 3 3 3.6332 - 3.1743 1.00 2742 131 0.1979 0.2357 REMARK 3 4 3.1743 - 2.8842 1.00 2697 150 0.2216 0.2657 REMARK 3 5 2.8842 - 2.6775 1.00 2699 132 0.2183 0.2549 REMARK 3 6 2.6775 - 2.5197 1.00 2694 136 0.2111 0.2849 REMARK 3 7 2.5197 - 2.3936 1.00 2678 140 0.2148 0.2755 REMARK 3 8 2.3936 - 2.2894 1.00 2663 141 0.2246 0.2734 REMARK 3 9 2.2894 - 2.2013 1.00 2663 143 0.2233 0.2804 REMARK 3 10 2.2013 - 2.1253 1.00 2667 126 0.2437 0.2644 REMARK 3 11 2.1253 - 2.0589 0.99 2617 143 0.2633 0.3397 REMARK 3 12 2.0589 - 2.0000 0.97 2586 133 0.2874 0.3346 REMARK 3 13 2.0000 - 1.9474 0.90 2392 120 0.2984 0.4002 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.350 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 56.03 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 : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 251 THROUGH 575) REMARK 3 ORIGIN FOR THE GROUP (A): -13.2684 -10.6574 14.9908 REMARK 3 T TENSOR REMARK 3 T11: 0.3550 T22: 0.4508 REMARK 3 T33: 0.4050 T12: 0.0287 REMARK 3 T13: -0.0478 T23: -0.0705 REMARK 3 L TENSOR REMARK 3 L11: 1.6591 L22: 1.6711 REMARK 3 L33: 1.3326 L12: 0.0921 REMARK 3 L13: -0.7349 L23: 0.3343 REMARK 3 S TENSOR REMARK 3 S11: 0.0464 S12: -0.1533 S13: 0.0993 REMARK 3 S21: 0.2153 S22: 0.1002 S23: -0.1085 REMARK 3 S31: -0.0129 S32: 0.1495 S33: -0.0001 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN 'T' AND RESID 1 THROUGH 4) REMARK 3 ORIGIN FOR THE GROUP (A): -28.1764 -24.9673 27.4559 REMARK 3 T TENSOR REMARK 3 T11: 0.6704 T22: 0.7281 REMARK 3 T33: 0.4137 T12: 0.0179 REMARK 3 T13: 0.0157 T23: 0.1379 REMARK 3 L TENSOR REMARK 3 L11: 0.1601 L22: 0.4240 REMARK 3 L33: 0.0313 L12: -0.1510 REMARK 3 L13: -0.0453 L23: -0.0451 REMARK 3 S TENSOR REMARK 3 S11: 0.1659 S12: -0.3731 S13: -0.2041 REMARK 3 S21: -0.3107 S22: -0.0836 S23: 0.7504 REMARK 3 S31: 0.5833 S32: -0.4684 S33: -0.0031 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN 'T' AND RESID 5 THROUGH 11) REMARK 3 ORIGIN FOR THE GROUP (A): -27.6619 -8.9965 11.9812 REMARK 3 T TENSOR REMARK 3 T11: 0.5380 T22: 0.5393 REMARK 3 T33: 0.4453 T12: 0.1174 REMARK 3 T13: 0.0363 T23: -0.0209 REMARK 3 L TENSOR REMARK 3 L11: 0.5884 L22: 2.5821 REMARK 3 L33: 8.3672 L12: -0.6527 REMARK 3 L13: 1.7110 L23: -4.4894 REMARK 3 S TENSOR REMARK 3 S11: 0.1308 S12: -0.6681 S13: 0.0240 REMARK 3 S21: 1.0771 S22: 0.8623 S23: 0.5479 REMARK 3 S31: -1.7164 S32: -0.7963 S33: 0.4125 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN 'P' AND RESID 1 THROUGH 7) REMARK 3 ORIGIN FOR THE GROUP (A): -24.3236 -13.8853 9.8719 REMARK 3 T TENSOR REMARK 3 T11: 0.4344 T22: 0.5299 REMARK 3 T33: 0.3896 T12: 0.0250 REMARK 3 T13: -0.0270 T23: -0.0480 REMARK 3 L TENSOR REMARK 3 L11: 0.1395 L22: 0.3590 REMARK 3 L33: 0.3020 L12: -0.0367 REMARK 3 L13: -0.1417 L23: -0.1743 REMARK 3 S TENSOR REMARK 3 S11: 0.1771 S12: -0.7326 S13: 0.0242 REMARK 3 S21: 0.2337 S22: -0.1883 S23: -0.1260 REMARK 3 S31: -0.4604 S32: -0.1321 S33: -0.0006 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN 'D' AND RESID 1 THROUGH 4) REMARK 3 ORIGIN FOR THE GROUP (A): -19.6262 -27.8986 30.0893 REMARK 3 T TENSOR REMARK 3 T11: 0.7937 T22: 0.7624 REMARK 3 T33: 0.4183 T12: 0.0051 REMARK 3 T13: 0.1598 T23: 0.1258 REMARK 3 L TENSOR REMARK 3 L11: 1.2498 L22: 0.7997 REMARK 3 L33: 1.9091 L12: 0.8963 REMARK 3 L13: 1.2046 L23: 1.1969 REMARK 3 S TENSOR REMARK 3 S11: -0.0109 S12: 0.1178 S13: -0.6532 REMARK 3 S21: 0.3734 S22: 0.1990 S23: -0.3766 REMARK 3 S31: 0.5085 S32: 0.4075 S33: 0.1801 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 7M4F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-MAR-21. REMARK 100 THE DEPOSITION ID IS D_1001310100. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-DEC-17 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 : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36574 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.947 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 (%) : 98.8 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.06300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.98 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.7 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : 0.55900 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 (%): 56.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.84 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 27.93450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 71.04350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.03250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 71.04350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.93450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.03250 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: 5070 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16750 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -82.0 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 465 VAL A 536 REMARK 465 VAL A 537 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 ALA 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 HIS A 252 CG ND1 CD2 CE1 NE2 REMARK 470 LEU A 254 CG CD1 CD2 REMARK 470 ILE A 256 CG1 CG2 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 LYS A 265 CD CE NZ REMARK 470 ARG A 275 NH1 NH2 REMARK 470 LYS A 281 NZ REMARK 470 LEU A 286 CD1 CD2 REMARK 470 LYS A 287 CG CD CE NZ REMARK 470 SER A 288 OG REMARK 470 PHE A 289 CD1 CD2 CE1 CE2 CZ REMARK 470 HIS A 290 ND1 CD2 CE1 NE2 REMARK 470 LYS A 291 CG CD 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 302 CD1 REMARK 470 LYS A 307 CG CD CE NZ REMARK 470 ARG A 308 CD NE CZ NH1 NH2 REMARK 470 ILE A 313 CD1 REMARK 470 ILE A 314 CG1 CG2 CD1 REMARK 470 ILE A 316 CG1 CG2 CD1 REMARK 470 LEU A 317 CG CD1 CD2 REMARK 470 GLU A 318 CD OE1 OE2 REMARK 470 SER A 319 OG 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 GLU A 330 OE1 OE2 REMARK 470 GLU A 385 CD OE1 OE2 REMARK 470 GLU A 390 OE1 OE2 REMARK 470 GLN A 397 CD OE1 NE2 REMARK 470 LYS A 401 CG CD CE NZ REMARK 470 PHE A 406 CD1 CD2 CE1 CE2 CZ REMARK 470 SER A 408 OG REMARK 470 LEU A 411 CD1 CD2 REMARK 470 LYS A 422 CE NZ REMARK 470 ARG A 438 CD NE CZ NH1 NH2 REMARK 470 SER A 439 OG REMARK 470 ARG A 441 CG CD NE CZ NH1 NH2 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 ARG A 452 NH1 NH2 REMARK 470 GLN A 453 CB CG CD OE1 NE2 REMARK 470 LYS A 463 CE NZ REMARK 470 GLU A 470 CG CD OE1 OE2 REMARK 470 ARG A 485 NH1 NH2 REMARK 470 ALA A 535 O REMARK 470 PRO A 547 CG CD REMARK 470 LYS A 557 CD CE NZ REMARK 470 ARG A 568 CZ NH1 NH2 REMARK 470 GLU A 572 CG CD OE1 OE2 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 DA P 2 O3' DA P 2 C3' -0.049 REMARK 500 DG D 1 P DG D 1 OP3 -0.126 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 DG T 2 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 DA T 5 O5' - P - OP1 ANGL. DEV. = -10.2 DEGREES REMARK 500 DG T 11 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG D 1 O4' - C1' - C2' ANGL. DEV. = 3.3 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 HIS A 252 5.44 -68.12 REMARK 500 GLU A 318 -71.83 -90.35 REMARK 500 GLU A 330 -19.61 -45.96 REMARK 500 ARG A 358 -9.03 -140.12 REMARK 500 CYS A 415 -135.95 -114.58 REMARK 500 ARG A 438 -35.41 -131.06 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 NA A 602 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 339 O REMARK 620 2 ILE A 341 O 96.6 REMARK 620 3 ALA A 344 O 95.2 86.1 REMARK 620 4 DA P 5 OP1 163.9 98.5 91.6 REMARK 620 5 HOH P 103 O 77.6 171.6 88.5 88.1 REMARK 620 6 HOH P 115 O 90.5 97.2 173.1 81.9 88.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 601 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 427 OD1 REMARK 620 2 ASP A 427 OD2 36.8 REMARK 620 3 ASP A 429 OD1 84.4 114.9 REMARK 620 4 ASP A 490 OD2 147.0 118.4 96.7 REMARK 620 5 DC P 6 O3' 121.6 129.2 100.1 90.8 REMARK 620 6 DC P 7 OP1 61.8 85.5 86.0 151.2 60.5 REMARK 620 7 HOH P 113 O 79.3 54.2 161.4 101.9 81.1 78.4 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 604 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 427 OD1 REMARK 620 2 ASP A 427 OD1 12.2 REMARK 620 3 ASP A 429 OD2 107.4 114.9 REMARK 620 4 PPV A 605 O21 138.0 140.4 96.8 REMARK 620 5 PPV A 605 O22 77.9 72.4 167.8 72.8 REMARK 620 6 HOH A 702 O 73.8 82.0 102.8 67.6 67.6 REMARK 620 7 DC P 7 OP1 102.7 91.4 102.8 104.7 86.4 154.0 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 603 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 784 O REMARK 620 2 HOH A 792 O 153.4 REMARK 620 N 1 DBREF 7M4F A 242 575 UNP Q9UGP5 DPOLL_HUMAN 242 575 DBREF 7M4F T 1 11 PDB 7M4F 7M4F 1 11 DBREF 7M4F P 1 7 PDB 7M4F 7M4F 1 7 DBREF 7M4F D 1 4 PDB 7M4F 7M4F 1 4 SEQADV 7M4F LYS A 463 UNP Q9UGP5 SER 463 CONFLICT SEQADV 7M4F GLY A 464 UNP Q9UGP5 GLN 464 CONFLICT SEQADV 7M4F A UNP Q9UGP5 GLU 466 DELETION SEQADV 7M4F A UNP Q9UGP5 ASN 467 DELETION SEQADV 7M4F A UNP Q9UGP5 GLY 468 DELETION SEQADV 7M4F A UNP Q9UGP5 GLN 469 DELETION SEQADV 7M4F A UNP Q9UGP5 GLN 470 DELETION SEQADV 7M4F THR A 471 UNP Q9UGP5 GLN 471 CONFLICT SEQADV 7M4F 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 DC SEQRES 1 D 4 DG DC DC DG HET NA A 601 1 HET NA A 602 1 HET NA A 603 1 HET MG A 604 1 HET PPV A 605 9 HET CL A 606 1 HETNAM NA SODIUM ION HETNAM MG MAGNESIUM ION HETNAM PPV PYROPHOSPHATE HETNAM CL CHLORIDE ION FORMUL 5 NA 3(NA 1+) FORMUL 8 MG MG 2+ FORMUL 9 PPV H4 O7 P2 FORMUL 10 CL CL 1- FORMUL 11 HOH *129(H2 O) HELIX 1 AA1 ASN A 253 GLN A 270 1 18 HELIX 2 AA2 ASP A 272 LYS A 287 1 16 HELIX 3 AA3 SER A 295 CYS A 300 1 6 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 GLU A 385 1 7 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 THR A 433 N LEU A 411 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 LYS A 463 -1 N THR A 458 O VAL A 476 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 VAL A 550 LEU A 551 -1 O LEU A 551 N LEU A 532 LINK O SER A 339 NA NA A 602 1555 1555 2.39 LINK O ILE A 341 NA NA A 602 1555 1555 2.44 LINK O ALA A 344 NA NA A 602 1555 1555 2.22 LINK OD1BASP A 427 NA NA A 601 1555 1555 3.13 LINK OD2AASP A 427 NA NA A 601 1555 1555 2.05 LINK OD1AASP A 427 MG MG A 604 1555 1555 1.96 LINK OD1BASP A 427 MG MG A 604 1555 1555 1.91 LINK OD1 ASP A 429 NA NA A 601 1555 1555 2.19 LINK OD2 ASP A 429 MG MG A 604 1555 1555 2.11 LINK OD2 ASP A 490 NA NA A 601 1555 1555 2.48 LINK NA NA A 601 O3' DC P 6 1555 1555 2.70 LINK NA NA A 601 OP1 DC P 7 1555 1555 2.43 LINK NA NA A 601 O BHOH P 113 1555 1555 2.40 LINK NA NA A 602 OP1 DA P 5 1555 1555 2.50 LINK NA NA A 602 O HOH P 103 1555 1555 2.60 LINK NA NA A 602 O HOH P 115 1555 1555 2.38 LINK NA NA A 603 O HOH A 784 1555 1555 3.14 LINK NA NA A 603 O HOH A 792 1555 1555 2.71 LINK MG MG A 604 O21 PPV A 605 1555 1555 2.12 LINK MG MG A 604 O22 PPV A 605 1555 1555 2.34 LINK MG MG A 604 O HOH A 702 1555 1555 2.05 LINK MG MG A 604 OP1 DC P 7 1555 1555 2.16 CISPEP 1 GLY A 508 SER A 509 0 2.76 CRYST1 55.869 62.065 142.087 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 0.017899 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016112 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007038 0.00000