HEADER TRANSFERASE 10-MAR-21 7M08 TITLE POST-CATALYTIC NICKED COMPLEX OF DNA POLYMERASE LAMBDA WITH BOUND 1-NT TITLE 2 GAPPED SSB SUBSTRATE 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*GP*TP*AP*CP*TP*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*AP*CP*T)-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 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_STRAIN: ROSETTA2 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEXM; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 18 ORGANISM_TAXID: 32630; SOURCE 19 MOL_ID: 4; SOURCE 20 SYNTHETIC: YES; SOURCE 21 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 22 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 2 18-OCT-23 7M08 1 JRNL REVDAT 1 16-MAR-22 7M08 0 JRNL AUTH A.M.KAMINSKI,K.BEBENEK,T.A.KUNKEL,L.C.PEDERSEN JRNL TITL COMPREHENSIVE STRUCTURAL SURVEY OF DNA DOUBLE-STRAND BREAK JRNL TITL 2 SYNAPSIS BY DNA POLYMERASE LAMBDA JRNL REF NOT PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.70 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.82 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 52835 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2642 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 43.8200 - 4.5300 0.99 2843 152 0.1821 0.2112 REMARK 3 2 4.5300 - 3.6000 0.99 2709 139 0.1474 0.1766 REMARK 3 3 3.6000 - 3.1400 1.00 2674 146 0.1724 0.1941 REMARK 3 4 3.1400 - 2.8500 1.00 2673 138 0.1881 0.1972 REMARK 3 5 2.8500 - 2.6500 0.99 2645 138 0.1931 0.2194 REMARK 3 6 2.6500 - 2.4900 1.00 2636 138 0.1852 0.2110 REMARK 3 7 2.4900 - 2.3700 1.00 2668 142 0.1777 0.1994 REMARK 3 8 2.3700 - 2.2700 1.00 2639 138 0.1834 0.2047 REMARK 3 9 2.2700 - 2.1800 1.00 2620 147 0.1992 0.2320 REMARK 3 10 2.1800 - 2.1000 1.00 2637 122 0.2122 0.2252 REMARK 3 11 2.1000 - 2.0400 1.00 2620 150 0.2013 0.2236 REMARK 3 12 2.0400 - 1.9800 1.00 2597 149 0.1921 0.2063 REMARK 3 13 1.9800 - 1.9300 1.00 2623 115 0.1871 0.2147 REMARK 3 14 1.9300 - 1.8800 1.00 2628 136 0.1837 0.2132 REMARK 3 15 1.8800 - 1.8400 1.00 2603 145 0.2018 0.2170 REMARK 3 16 1.8400 - 1.8000 1.00 2616 136 0.2258 0.2600 REMARK 3 17 1.8000 - 1.7600 1.00 2595 129 0.2537 0.2620 REMARK 3 18 1.7600 - 1.7300 1.00 2619 156 0.2854 0.3101 REMARK 3 19 1.7300 - 1.7000 0.99 2548 126 0.3340 0.3493 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) : 0.213 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.186 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.57 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.17 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 : 0.007 3130 REMARK 3 ANGLE : 0.824 4349 REMARK 3 CHIRALITY : 0.051 481 REMARK 3 PLANARITY : 0.006 488 REMARK 3 DIHEDRAL : 12.486 935 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 239:329 REMARK 3 ORIGIN FOR THE GROUP (A): -7.5116 26.3965 -25.7281 REMARK 3 T TENSOR REMARK 3 T11: 0.3758 T22: 0.3936 REMARK 3 T33: 0.2876 T12: -0.0906 REMARK 3 T13: 0.1029 T23: -0.0323 REMARK 3 L TENSOR REMARK 3 L11: 0.4036 L22: 0.6670 REMARK 3 L33: 0.7704 L12: 0.2070 REMARK 3 L13: -0.0703 L23: -0.1609 REMARK 3 S TENSOR REMARK 3 S11: -0.1015 S12: 0.3062 S13: 0.0032 REMARK 3 S21: -0.2942 S22: 0.3081 S23: -0.2743 REMARK 3 S31: -0.1089 S32: 0.2587 S33: 0.0021 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND RESID 330:386 REMARK 3 ORIGIN FOR THE GROUP (A): -13.4613 20.0998 0.6717 REMARK 3 T TENSOR REMARK 3 T11: 0.1356 T22: 0.1417 REMARK 3 T33: 0.1543 T12: 0.0038 REMARK 3 T13: -0.0077 T23: -0.0290 REMARK 3 L TENSOR REMARK 3 L11: 0.5316 L22: 0.7237 REMARK 3 L33: 0.4563 L12: 0.2849 REMARK 3 L13: 0.0155 L23: -0.0608 REMARK 3 S TENSOR REMARK 3 S11: -0.0221 S12: -0.1100 S13: 0.1357 REMARK 3 S21: 0.0100 S22: 0.0736 S23: -0.0425 REMARK 3 S31: 0.0437 S32: -0.1259 S33: 0.0029 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND RESID 387:495 REMARK 3 ORIGIN FOR THE GROUP (A): -12.2044 -5.1371 -7.4695 REMARK 3 T TENSOR REMARK 3 T11: 0.1623 T22: 0.1256 REMARK 3 T33: 0.2409 T12: -0.0179 REMARK 3 T13: -0.0148 T23: -0.0191 REMARK 3 L TENSOR REMARK 3 L11: 0.7917 L22: 1.0218 REMARK 3 L33: 1.7213 L12: -0.6002 REMARK 3 L13: 0.3289 L23: -0.2027 REMARK 3 S TENSOR REMARK 3 S11: 0.0491 S12: -0.0201 S13: -0.3026 REMARK 3 S21: -0.0178 S22: 0.0258 S23: 0.0588 REMARK 3 S31: 0.1514 S32: 0.0269 S33: -0.0010 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN A AND RESID 496:575 REMARK 3 ORIGIN FOR THE GROUP (A): -18.9927 1.8097 -27.8341 REMARK 3 T TENSOR REMARK 3 T11: 0.2491 T22: 0.2436 REMARK 3 T33: 0.1610 T12: 0.0290 REMARK 3 T13: -0.0253 T23: -0.0565 REMARK 3 L TENSOR REMARK 3 L11: 0.7362 L22: 0.4047 REMARK 3 L33: 0.5354 L12: -0.2571 REMARK 3 L13: 0.0370 L23: -0.0189 REMARK 3 S TENSOR REMARK 3 S11: 0.0812 S12: 0.3196 S13: -0.1083 REMARK 3 S21: -0.3006 S22: -0.0310 S23: -0.0165 REMARK 3 S31: 0.0180 S32: 0.1127 S33: 0.0340 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN T OR CHAIN P OR CHAIN D REMARK 3 ORIGIN FOR THE GROUP (A): -25.0193 16.3843 -18.0297 REMARK 3 T TENSOR REMARK 3 T11: 0.1648 T22: 0.1994 REMARK 3 T33: 0.1433 T12: 0.0265 REMARK 3 T13: -0.0237 T23: -0.0006 REMARK 3 L TENSOR REMARK 3 L11: 0.5813 L22: 0.2133 REMARK 3 L33: 0.5606 L12: 0.2450 REMARK 3 L13: -0.4143 L23: 0.5480 REMARK 3 S TENSOR REMARK 3 S11: -0.0042 S12: 0.1673 S13: -0.0173 REMARK 3 S21: -0.0956 S22: 0.0083 S23: 0.2061 REMARK 3 S31: -0.1014 S32: -0.1524 S33: -0.0390 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 7M08 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_1000255336. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-SEP-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 : 52904 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07800 REMARK 200 FOR THE DATA SET : 26.1000 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.67700 REMARK 200 FOR SHELL : 1.620 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 (%): 52.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 37.5MM NA CACODYLATE PH 6.5, 150MM REMARK 280 KCL, 75MM MAGNESIUM ACETATE, 7.5% (W/V) PEG8000, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K 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 28.06800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 70.09450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.93100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 70.09450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.06800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.93100 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: 5700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16650 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -95.0 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 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 LEU A 236 REMARK 465 ASP A 237 REMARK 465 LYS A 238 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 CYS A 543 REMARK 465 LYS A 544 REMARK 465 VAL A 545 REMARK 465 GLY A 546 REMARK 465 PRO A 547 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 TRP A 239 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 239 CZ3 CH2 REMARK 470 VAL A 240 CG1 CG2 REMARK 470 LYS A 248 CG CD CE NZ REMARK 470 THR A 250 OG1 CG2 REMARK 470 LEU A 254 CG CD1 CD2 REMARK 470 HIS A 255 CG ND1 CD2 CE1 NE2 REMARK 470 GLU A 258 CD OE1 OE2 REMARK 470 LYS A 259 NZ REMARK 470 GLU A 261 CD OE1 OE2 REMARK 470 LYS A 265 CD CE NZ REMARK 470 LYS A 273 NZ REMARK 470 VAL A 293 CG1 CG2 REMARK 470 GLN A 297 CG CD OE1 NE2 REMARK 470 LYS A 307 CG CD CE NZ REMARK 470 ARG A 308 NE CZ NH1 NH2 REMARK 470 GLU A 311 OE1 OE2 REMARK 470 ILE A 316 CG1 CG2 CD1 REMARK 470 LEU A 317 CD1 CD2 REMARK 470 GLU A 318 CG CD OE1 OE2 REMARK 470 ARG A 323 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 330 CD OE1 OE2 REMARK 470 GLU A 336 CD OE1 OE2 REMARK 470 GLU A 390 CG CD OE1 OE2 REMARK 470 LYS A 401 CG CD CE NZ REMARK 470 LEU A 411 CD1 CD2 REMARK 470 LYS A 422 NZ REMARK 470 ARG A 438 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 441 CD NE CZ NH1 NH2 REMARK 470 ILE A 443 CG1 CG2 CD1 REMARK 470 GLN A 453 CG CD OE1 NE2 REMARK 470 GLU A 466 CG CD OE1 OE2 REMARK 470 LYS A 521 CE NZ REMARK 470 LYS A 523 NZ REMARK 470 GLU A 529 OE1 OE2 REMARK 470 LYS A 557 CE NZ REMARK 470 GLU A 569 CD OE1 OE2 REMARK 470 GLU A 572 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 OD2 ASP A 382 O HOH A 701 2.05 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 -0.122 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. = 2.4 DEGREES REMARK 500 DC T 4 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT T 7 O4' - C1' - N1 ANGL. DEV. = 2.4 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 -141.69 -110.90 REMARK 500 ARG A 438 -39.28 -136.03 REMARK 500 SER A 463 95.70 -164.84 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 941 DISTANCE = 5.92 ANGSTROMS REMARK 525 HOH A 942 DISTANCE = 6.48 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 603 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN A 247 O REMARK 620 2 THR A 250 O 104.9 REMARK 620 3 LYS A 287 O 90.0 90.3 REMARK 620 4 PHE A 289 O 138.4 116.7 89.6 REMARK 620 N 1 2 3 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 CYS A 300 O REMARK 620 2 ILE A 302 O 85.3 REMARK 620 3 ILE A 305 O 92.8 79.8 REMARK 620 4 HOH A 885 O 84.4 75.3 155.1 REMARK 620 5 DC D 3 OP1 168.9 85.1 91.1 87.7 REMARK 620 N 1 2 3 4 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 SER A 339 O REMARK 620 2 ILE A 341 O 97.8 REMARK 620 3 ALA A 344 O 88.2 81.5 REMARK 620 4 HOH A 897 O 91.0 91.7 173.0 REMARK 620 5 DA P 5 OP1 167.1 94.4 89.6 92.7 REMARK 620 6 HOH P 109 O 77.6 165.4 84.4 102.2 89.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 606 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 427 OD1 REMARK 620 2 ASP A 427 OD2 47.4 REMARK 620 3 ASP A 429 OD1 89.1 132.6 REMARK 620 4 ASP A 490 OD2 125.0 86.0 113.4 REMARK 620 5 DC P 6 O3' 129.9 116.3 106.0 92.8 REMARK 620 6 DT P 7 OP1 68.3 86.3 94.8 147.7 63.1 REMARK 620 N 1 2 3 4 5 DBREF 7M08 A 234 575 UNP Q9UGP5 DPOLL_HUMAN 234 575 DBREF 7M08 T 1 11 PDB 7M08 7M08 1 11 DBREF 7M08 P 1 7 PDB 7M08 7M08 1 7 DBREF 7M08 D 1 4 PDB 7M08 7M08 1 4 SEQADV 7M08 GLY A 230 UNP Q9UGP5 EXPRESSION TAG SEQADV 7M08 SER A 231 UNP Q9UGP5 EXPRESSION TAG SEQADV 7M08 ALA A 232 UNP Q9UGP5 EXPRESSION TAG SEQADV 7M08 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 11 DC DG DG DC DA DG DT DA DC DT DG SEQRES 1 P 7 DC DA DG DT DA DC DT SEQRES 1 D 4 DG DC DC DG HET NA A 601 1 HET NA A 602 1 HET NA A 603 1 HET CL A 604 1 HET CL A 605 1 HET MG A 606 1 HET EDO A 607 4 HET ACT A 608 4 HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETNAM MG MAGNESIUM ION HETNAM EDO 1,2-ETHANEDIOL HETNAM ACT ACETATE ION HETSYN EDO ETHYLENE GLYCOL FORMUL 5 NA 3(NA 1+) FORMUL 8 CL 2(CL 1-) FORMUL 10 MG MG 2+ FORMUL 11 EDO C2 H6 O2 FORMUL 12 ACT C2 H3 O2 1- FORMUL 13 HOH *336(H2 O) HELIX 1 AA1 TRP A 239 GLN A 243 5 5 HELIX 2 AA2 PRO A 244 ALA A 249 5 6 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 SER A 301 1 7 HELIX 6 AA6 GLY A 306 GLY A 320 1 15 HELIX 7 AA7 LEU A 322 HIS A 327 5 6 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 SER A 381 GLU A 385 5 5 HELIX 13 AB4 ARG A 389 ALA A 405 1 17 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 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 428 SHEET 4 AA2 5 LYS A 472 CYS A 477 -1 N CYS A 477 O ARG A 487 SHEET 5 AA2 5 LEU A 457 VAL A 462 -1 N ASP A 459 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 GLN A 247 NA NA A 603 1555 1555 2.61 LINK O THR A 250 NA NA A 603 1555 1555 2.61 LINK O LYS A 287 NA NA A 603 1555 1555 2.61 LINK O PHE A 289 NA NA A 603 1555 1555 2.83 LINK O CYS A 300 NA NA A 602 1555 1555 2.47 LINK O ILE A 302 NA NA A 602 1555 1555 2.83 LINK O ILE A 305 NA NA A 602 1555 1555 2.58 LINK O SER A 339 NA NA A 601 1555 1555 2.38 LINK O ILE A 341 NA NA A 601 1555 1555 2.63 LINK O ALA A 344 NA NA A 601 1555 1555 2.43 LINK OD1 ASP A 427 MG MG A 606 1555 1555 2.98 LINK OD2 ASP A 427 MG MG A 606 1555 1555 2.09 LINK OD1 ASP A 429 MG MG A 606 1555 1555 2.00 LINK OD2 ASP A 490 MG MG A 606 1555 1555 1.78 LINK NA NA A 601 O HOH A 897 1555 1555 2.47 LINK NA NA A 601 OP1 DA P 5 1555 1555 2.54 LINK NA NA A 601 O HOH P 109 1555 1555 2.62 LINK NA NA A 602 O HOH A 885 1555 1555 2.50 LINK NA NA A 602 OP1 DC D 3 1555 1555 2.93 LINK MG MG A 606 O3' DC P 6 1555 1555 2.75 LINK MG MG A 606 OP1 DT P 7 1555 1555 1.85 CISPEP 1 GLY A 508 SER A 509 0 1.87 CRYST1 56.136 59.862 140.189 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 0.017814 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016705 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007133 0.00000