HEADER TRANSFERASE/DNA 11-MAY-12 4F50 TITLE Y-FAMILY DNA POLYMERASE CHIMERA DBH-DBH-DPO4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE IV; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: POL IV; COMPND 5 EC: 2.7.7.7; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*GP*GP*GP*AP*AP*GP*CP*CP*GP*GP*C)-3'); COMPND 9 CHAIN: P; COMPND 10 ENGINEERED: YES; COMPND 11 OTHER_DETAILS: PRIMER DNA; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'-D(*CP*CP*GP*CP*CP*T*GP*GP*CP*TP*TP*CP*CP*C)-3'); COMPND 14 CHAIN: T; COMPND 15 ENGINEERED: YES; COMPND 16 OTHER_DETAILS: TEMPLATE DNA SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SULFOLOBUS ACIDOCALDARIUS, SULFOLOBUS SOURCE 3 SOLFATARICUS; SOURCE 4 ORGANISM_TAXID: 330779, 273057; SOURCE 5 STRAIN: ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770; SOURCE 6 GENE: DBH, DPO4, DPO4 (S. SOLFATARICUS) AND DBH (S. ACIDOCALDARIUS), SOURCE 7 SACI_0554, SSO24 48; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: BLR(DE3)PLYSS; SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PKKT7-H; SOURCE 12 MOL_ID: 2; SOURCE 13 SYNTHETIC: YES; SOURCE 14 MOL_ID: 3; SOURCE 15 SYNTHETIC: YES KEYWDS Y-FAMILY POLYMERASE, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.D.PATA,R.C.WILSON REVDAT 6 28-FEB-24 4F50 1 REMARK SEQADV LINK REVDAT 5 16-AUG-17 4F50 1 SOURCE REMARK REVDAT 4 12-FEB-14 4F50 1 SOURCE REVDAT 3 29-JAN-14 4F50 1 SOURCE REVDAT 2 13-FEB-13 4F50 1 JRNL REVDAT 1 02-JAN-13 4F50 0 JRNL AUTH R.C.WILSON,M.A.JACKSON,J.D.PATA JRNL TITL Y-FAMILY POLYMERASE CONFORMATION IS A MAJOR DETERMINANT OF JRNL TITL 2 FIDELITY AND TRANSLESION SPECIFICITY. JRNL REF STRUCTURE V. 21 20 2013 JRNL REFN ISSN 0969-2126 JRNL PMID 23245850 JRNL DOI 10.1016/J.STR.2012.11.005 REMARK 2 REMARK 2 RESOLUTION. 2.22 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.3_928) 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) : 2.22 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.47 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.490 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 27377 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.269 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 1365 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 28.4707 - 4.7649 0.97 2761 146 0.1906 0.2378 REMARK 3 2 4.7649 - 3.7849 1.00 2718 143 0.1685 0.2110 REMARK 3 3 3.7849 - 3.3073 1.00 2675 141 0.1959 0.2616 REMARK 3 4 3.3073 - 3.0053 1.00 2668 139 0.2133 0.3028 REMARK 3 5 3.0053 - 2.7901 1.00 2633 139 0.2442 0.3030 REMARK 3 6 2.7901 - 2.6257 0.99 2621 139 0.2700 0.3661 REMARK 3 7 2.6257 - 2.4943 0.99 2620 135 0.2776 0.3350 REMARK 3 8 2.4943 - 2.3857 0.99 2604 137 0.2907 0.3747 REMARK 3 9 2.3857 - 2.2939 0.97 2522 136 0.3075 0.3583 REMARK 3 10 2.2939 - 2.2150 0.83 2190 110 0.3062 0.3220 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.98 REMARK 3 K_SOL : 0.33 REMARK 3 B_SOL : 56.50 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.320 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.180 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.28010 REMARK 3 B22 (A**2) : 5.28010 REMARK 3 B33 (A**2) : -10.56020 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 3254 REMARK 3 ANGLE : 1.227 4474 REMARK 3 CHIRALITY : 0.075 512 REMARK 3 PLANARITY : 0.005 491 REMARK 3 DIHEDRAL : 18.769 1287 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ( CHAIN P AND RESID 1:11 ) OR ( CHAIN T AND RESID REMARK 3 1:14 ) REMARK 3 ORIGIN FOR THE GROUP (A): -27.0936 2.0114 -14.7811 REMARK 3 T TENSOR REMARK 3 T11: 0.9725 T22: 0.5375 REMARK 3 T33: 0.6557 T12: 0.2848 REMARK 3 T13: -0.0172 T23: -0.1502 REMARK 3 L TENSOR REMARK 3 L11: 0.2579 L22: 3.1986 REMARK 3 L33: -0.0084 L12: -0.6328 REMARK 3 L13: 0.0408 L23: 0.1794 REMARK 3 S TENSOR REMARK 3 S11: 0.0334 S12: 0.6333 S13: 0.0414 REMARK 3 S21: 0.1374 S22: 0.0081 S23: -0.6212 REMARK 3 S31: 0.1531 S32: 0.0868 S33: 0.0007 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN A AND RESID 1:168 ) REMARK 3 ORIGIN FOR THE GROUP (A): -36.3451 -24.1286 -15.9354 REMARK 3 T TENSOR REMARK 3 T11: 0.4410 T22: 0.4103 REMARK 3 T33: 0.3495 T12: 0.1667 REMARK 3 T13: 0.1114 T23: 0.0593 REMARK 3 L TENSOR REMARK 3 L11: 0.9398 L22: 4.0786 REMARK 3 L33: 4.0844 L12: 0.3095 REMARK 3 L13: -0.7698 L23: -0.1451 REMARK 3 S TENSOR REMARK 3 S11: 0.0116 S12: -0.1221 S13: -0.1299 REMARK 3 S21: 0.9108 S22: 0.4240 S23: 0.2072 REMARK 3 S31: 0.0937 S32: -0.1675 S33: -0.2642 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: ( CHAIN A AND RESID 169:246 ) REMARK 3 ORIGIN FOR THE GROUP (A): -29.3451 -8.0505 2.3041 REMARK 3 T TENSOR REMARK 3 T11: 1.4249 T22: 0.5594 REMARK 3 T33: 0.4967 T12: 0.2679 REMARK 3 T13: -0.1239 T23: -0.0363 REMARK 3 L TENSOR REMARK 3 L11: 3.3590 L22: 3.2475 REMARK 3 L33: 3.1603 L12: 0.1743 REMARK 3 L13: -0.5364 L23: -0.5293 REMARK 3 S TENSOR REMARK 3 S11: -0.2975 S12: -0.4884 S13: 0.4510 REMARK 3 S21: 1.8227 S22: 0.2211 S23: -0.1879 REMARK 3 S31: -0.3459 S32: 0.3262 S33: 0.1195 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: ( CHAIN A AND RESID 247:342 ) REMARK 3 ORIGIN FOR THE GROUP (A): -43.0788 3.0150 -29.8541 REMARK 3 T TENSOR REMARK 3 T11: 1.0635 T22: 1.2246 REMARK 3 T33: 0.9150 T12: 0.0176 REMARK 3 T13: -0.0435 T23: 0.5747 REMARK 3 L TENSOR REMARK 3 L11: 1.7118 L22: 3.8364 REMARK 3 L33: 6.0726 L12: 0.2857 REMARK 3 L13: 0.1697 L23: -2.5482 REMARK 3 S TENSOR REMARK 3 S11: -0.5376 S12: 1.1683 S13: 1.0738 REMARK 3 S21: -0.0486 S22: 0.9103 S23: 1.1076 REMARK 3 S31: -0.2310 S32: -0.9642 S33: -0.4701 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 4F50 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-MAY-12. REMARK 100 THE DEPOSITION ID IS D_1000072462. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-OCT-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.1 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27408 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.215 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 9.700 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 31.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.22 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 79.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.35300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER IN PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEG-3350, 100 MM CA(OAC)2, 100 MM REMARK 280 HEPES, 2.5% GLYCEROL, PH 7.1, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.23700 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 62.24100 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 62.24100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 17.61850 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 62.24100 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 62.24100 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 52.85550 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 62.24100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 62.24100 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 17.61850 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 62.24100 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 62.24100 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 52.85550 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 35.23700 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20260 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, P, T 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 510 LIES ON A SPECIAL POSITION. 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 35 REMARK 465 ARG A 36 REMARK 465 THR A 37 REMARK 465 LYS A 38 REMARK 465 THR A 39 REMARK 465 GLU A 343 REMARK 465 ALA A 344 REMARK 465 ILE A 345 REMARK 465 GLY A 346 REMARK 465 LEU A 347 REMARK 465 ASP A 348 REMARK 465 LYS A 349 REMARK 465 PHE A 350 REMARK 465 PHE A 351 REMARK 465 ASP A 352 REMARK 465 THR A 353 REMARK 465 GLY A 354 REMARK 465 GLY A 355 REMARK 465 HIS A 356 REMARK 465 HIS A 357 REMARK 465 HIS A 358 REMARK 465 HIS A 359 REMARK 465 HIS A 360 REMARK 465 HIS A 361 REMARK 465 DC T 2 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 DT T 6 C5' C4' O4' C3' O3' C2' C1' REMARK 470 DT T 6 N1 C2 O2 N3 C4 O4 C5 REMARK 470 DT T 6 C7 C6 REMARK 470 DG T 7 P OP1 OP2 O5' C5' 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 NH2 ARG A 280 O HOH A 536 1.88 REMARK 500 O3' DC T 1 O HOH T 110 1.99 REMARK 500 N VAL A 166 O HOH A 539 2.05 REMARK 500 O HOH A 544 O HOH A 545 2.06 REMARK 500 OP2 DT T 6 O HOH T 107 2.09 REMARK 500 OP1 DG T 8 O HOH T 113 2.13 REMARK 500 O HOH A 517 O HOH A 545 2.15 REMARK 500 O ILE A 342 O HOH A 503 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 501 O HOH A 508 7554 1.93 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 P 9 O3' DG P 9 C3' -0.043 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 P 2 C3' - C2' - C1' ANGL. DEV. = -5.1 DEGREES REMARK 500 DG P 2 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DC T 5 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DG T 7 C1' - O4' - C4' ANGL. DEV. = -7.4 DEGREES REMARK 500 DG T 7 O4' - C1' - N9 ANGL. DEV. = 7.0 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 ARG A 77 77.54 -108.53 REMARK 500 SER A 103 -173.17 -171.62 REMARK 500 THR A 112 -70.37 -38.12 REMARK 500 SER A 208 54.72 -107.73 REMARK 500 SER A 235 112.30 -163.42 REMARK 500 LYS A 241 -175.34 -171.38 REMARK 500 ILE A 270 35.51 -77.31 REMARK 500 GLU A 271 -63.16 -142.66 REMARK 500 ASP A 278 -138.98 58.52 REMARK 500 PRO A 304 68.95 -68.13 REMARK 500 HIS A 305 144.29 -176.58 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 CA A 401 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 7 OD1 REMARK 620 2 GLU A 106 OE2 71.7 REMARK 620 3 HOH A 553 O 123.4 66.2 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4F4W RELATED DB: PDB REMARK 900 RELATED ID: 4F4X RELATED DB: PDB REMARK 900 RELATED ID: 4F4Y RELATED DB: PDB REMARK 900 RELATED ID: 4F4Z RELATED DB: PDB DBREF 4F50 A 1 246 UNP Q4JB80 DPO4_SULAC 1 246 DBREF 4F50 A 247 353 UNP Q97W02 DPO4_SULSO 246 352 DBREF 4F50 P 1 11 PDB 4F50 4F50 1 11 DBREF 4F50 T 1 14 PDB 4F50 4F50 1 14 SEQADV 4F50 GLY A 354 UNP Q97W02 EXPRESSION TAG SEQADV 4F50 GLY A 355 UNP Q97W02 EXPRESSION TAG SEQADV 4F50 HIS A 356 UNP Q97W02 EXPRESSION TAG SEQADV 4F50 HIS A 357 UNP Q97W02 EXPRESSION TAG SEQADV 4F50 HIS A 358 UNP Q97W02 EXPRESSION TAG SEQADV 4F50 HIS A 359 UNP Q97W02 EXPRESSION TAG SEQADV 4F50 HIS A 360 UNP Q97W02 EXPRESSION TAG SEQADV 4F50 HIS A 361 UNP Q97W02 EXPRESSION TAG SEQRES 1 A 361 MET ILE VAL ILE PHE VAL ASP PHE ASP TYR PHE PHE ALA SEQRES 2 A 361 GLN VAL GLU GLU VAL LEU ASN PRO GLN TYR LYS GLY LYS SEQRES 3 A 361 PRO LEU VAL VAL CYS VAL TYR SER GLY ARG THR LYS THR SEQRES 4 A 361 SER GLY ALA VAL ALA THR ALA ASN TYR GLU ALA ARG LYS SEQRES 5 A 361 LEU GLY VAL LYS ALA GLY MET PRO ILE ILE LYS ALA MET SEQRES 6 A 361 GLN ILE ALA PRO SER ALA ILE TYR VAL PRO MET ARG LYS SEQRES 7 A 361 PRO ILE TYR GLU ALA PHE SER ASN ARG ILE MET ASN LEU SEQRES 8 A 361 LEU ASN LYS HIS ALA ASP LYS ILE GLU VAL ALA SER ILE SEQRES 9 A 361 ASP GLU ALA TYR LEU ASP VAL THR ASN LYS VAL GLU GLY SEQRES 10 A 361 ASN PHE GLU ASN GLY ILE GLU LEU ALA ARG LYS ILE LYS SEQRES 11 A 361 GLN GLU ILE LEU GLU LYS GLU LYS ILE THR VAL THR VAL SEQRES 12 A 361 GLY VAL ALA PRO ASN LYS ILE LEU ALA LYS ILE ILE ALA SEQRES 13 A 361 ASP LYS SER LYS PRO ASN GLY LEU GLY VAL ILE ARG PRO SEQRES 14 A 361 THR GLU VAL GLN ASP PHE LEU ASN GLU LEU ASP ILE ASP SEQRES 15 A 361 GLU ILE PRO GLY ILE GLY SER VAL LEU ALA ARG ARG LEU SEQRES 16 A 361 ASN GLU LEU GLY ILE GLN LYS LEU ARG ASP ILE LEU SER SEQRES 17 A 361 LYS ASN TYR ASN GLU LEU GLU LYS ILE THR GLY LYS ALA SEQRES 18 A 361 LYS ALA LEU TYR LEU LEU LYS LEU ALA GLN ASN LYS TYR SEQRES 19 A 361 SER GLU PRO VAL GLU ASN LYS SER LYS ILE PRO HIS GLY SEQRES 20 A 361 ARG ILE VAL THR MET LYS ARG ASN SER ARG ASN LEU GLU SEQRES 21 A 361 GLU ILE LYS PRO TYR LEU PHE ARG ALA ILE GLU GLU SER SEQRES 22 A 361 TYR TYR LYS LEU ASP LYS ARG ILE PRO LYS ALA ILE HIS SEQRES 23 A 361 VAL VAL ALA VAL THR GLU ASP LEU ASP ILE VAL SER ARG SEQRES 24 A 361 GLY ARG THR PHE PRO HIS GLY ILE SER LYS GLU THR ALA SEQRES 25 A 361 TYR SER GLU SER VAL LYS LEU LEU GLN LYS ILE LEU GLU SEQRES 26 A 361 GLU ASP GLU ARG LYS ILE ARG ARG ILE GLY VAL ARG PHE SEQRES 27 A 361 SER LYS PHE ILE GLU ALA ILE GLY LEU ASP LYS PHE PHE SEQRES 28 A 361 ASP THR GLY GLY HIS HIS HIS HIS HIS HIS SEQRES 1 P 11 DG DG DG DA DA DG DC DC DG DG DC SEQRES 1 T 14 DC DC DG DC DC DT DG DG DC DT DT DC DC SEQRES 2 T 14 DC HET CA A 401 1 HETNAM CA CALCIUM ION FORMUL 4 CA CA 2+ FORMUL 5 HOH *74(H2 O) HELIX 1 1 TYR A 10 ASN A 20 1 11 HELIX 2 2 PRO A 21 LYS A 24 5 4 HELIX 3 3 ASN A 47 LEU A 53 1 7 HELIX 4 4 PRO A 60 GLN A 66 1 7 HELIX 5 5 ARG A 77 LYS A 94 1 18 HELIX 6 6 ASN A 118 LYS A 138 1 21 HELIX 7 7 ASN A 148 SER A 159 1 12 HELIX 8 8 GLU A 171 GLU A 178 1 8 HELIX 9 9 ASP A 180 ILE A 184 5 5 HELIX 10 10 GLY A 188 GLU A 197 1 10 HELIX 11 11 LYS A 202 LYS A 209 5 8 HELIX 12 12 ASN A 210 GLY A 219 1 10 HELIX 13 13 GLY A 219 GLN A 231 1 13 HELIX 14 14 ASN A 258 SER A 273 1 16 HELIX 15 15 SER A 273 ASP A 278 1 6 HELIX 16 16 SER A 308 GLU A 325 1 18 SHEET 1 A 6 LEU A 164 VAL A 166 0 SHEET 2 A 6 VAL A 141 ALA A 146 1 N VAL A 143 O GLY A 165 SHEET 3 A 6 VAL A 3 PHE A 8 -1 N ASP A 7 O THR A 142 SHEET 4 A 6 GLU A 106 ASP A 110 -1 O LEU A 109 N ILE A 4 SHEET 5 A 6 LYS A 98 SER A 103 -1 N GLU A 100 O TYR A 108 SHEET 6 A 6 LYS A 241 SER A 242 1 O LYS A 241 N VAL A 101 SHEET 1 B 3 ALA A 42 ALA A 46 0 SHEET 2 B 3 LEU A 28 VAL A 32 -1 N VAL A 30 O THR A 45 SHEET 3 B 3 ILE A 72 PRO A 75 1 O ILE A 72 N VAL A 29 SHEET 1 C 4 ILE A 249 SER A 256 0 SHEET 2 C 4 ILE A 331 SER A 339 -1 O ARG A 332 N MET A 252 SHEET 3 C 4 ALA A 284 THR A 291 -1 N VAL A 290 O ARG A 333 SHEET 4 C 4 ILE A 296 THR A 302 -1 O VAL A 297 N ALA A 289 LINK OD1 ASP A 7 CA CA A 401 1555 1555 3.10 LINK OE2 GLU A 106 CA CA A 401 1555 1555 3.08 LINK CA CA A 401 O HOH A 553 1555 1555 2.90 CISPEP 1 LYS A 160 PRO A 161 0 -8.56 SITE 1 AC1 3 ASP A 7 GLU A 106 HOH A 553 CRYST1 124.482 124.482 70.474 90.00 90.00 90.00 P 41 21 2 8 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 0.008033 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008033 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014190 0.00000