HEADER TRANSFERASE/DNA 17-SEP-20 7K5Q TITLE BST DNA POLYMERASE I TIME-RESOLVED STRUCTURE, 8 MIN POST DATP ADDITION COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(P*G*CP*GP*AP*TP*CP*AP*CP*GP*T)-3'); COMPND 3 CHAIN: P; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(P*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-3'); COMPND 7 CHAIN: T; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DNA POLYMERASE I; COMPND 11 CHAIN: A; COMPND 12 SYNONYM: BST DNA POLYMERASE I; COMPND 13 EC: 2.7.7.7; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630; SOURCE 9 MOL_ID: 3; SOURCE 10 ORGANISM_SCIENTIFIC: GEOBACILLUS STEAROTHERMOPHILUS; SOURCE 11 ORGANISM_TAXID: 1422; SOURCE 12 GENE: POLA; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DNA POLYMERASE, TRANSFERASE, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.CHIM,R.A.MEZA,A.M.TRINH,J.C.CHAPUT REVDAT 3 18-OCT-23 7K5Q 1 REMARK REVDAT 2 19-MAY-21 7K5Q 1 JRNL REVDAT 1 03-MAR-21 7K5Q 0 JRNL AUTH N.CHIM,R.A.MEZA,A.M.TRINH,K.YANG,J.C.CHAPUT JRNL TITL FOLLOWING REPLICATIVE DNA SYNTHESIS BY TIME-RESOLVED X-RAY JRNL TITL 2 CRYSTALLOGRAPHY. JRNL REF NAT COMMUN V. 12 2641 2021 JRNL REFN ESSN 2041-1723 JRNL PMID 33976175 JRNL DOI 10.1038/S41467-021-22937-Z REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.92 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 3 NUMBER OF REFLECTIONS : 57448 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.620 REMARK 3 FREE R VALUE TEST SET COUNT : 1504 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 39.9200 - 4.4500 0.96 5375 147 0.1667 0.1942 REMARK 3 2 4.4500 - 3.5300 0.97 5230 135 0.1649 0.2345 REMARK 3 3 3.5300 - 3.0800 0.99 5275 150 0.1821 0.2325 REMARK 3 4 3.0800 - 2.8000 0.99 5283 143 0.1991 0.2320 REMARK 3 5 2.8000 - 2.6000 0.99 5238 138 0.2025 0.2799 REMARK 3 6 2.6000 - 2.4500 1.00 5265 148 0.2034 0.2619 REMARK 3 7 2.4500 - 2.3300 1.00 5257 139 0.2159 0.2817 REMARK 3 8 2.3300 - 2.2200 0.68 3562 101 0.3593 0.4756 REMARK 3 9 2.2200 - 2.1400 0.95 4990 124 0.2585 0.3180 REMARK 3 10 2.1400 - 2.0600 1.00 5236 138 0.1961 0.2162 REMARK 3 11 2.0600 - 2.0000 1.00 5233 141 0.1987 0.2455 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) : 0.211 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.100 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.25 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.96 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 5275 REMARK 3 ANGLE : 0.866 7231 REMARK 3 CHIRALITY : 0.052 812 REMARK 3 PLANARITY : 0.005 854 REMARK 3 DIHEDRAL : 10.084 3133 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'P' AND (RESID 1 THROUGH 10 ) REMARK 3 ORIGIN FOR THE GROUP (A): 29.4049 28.0460 33.1804 REMARK 3 T TENSOR REMARK 3 T11: 0.8807 T22: 0.9387 REMARK 3 T33: 0.5308 T12: 0.0751 REMARK 3 T13: 0.0186 T23: -0.1867 REMARK 3 L TENSOR REMARK 3 L11: 2.2020 L22: 4.5478 REMARK 3 L33: 4.9285 L12: -1.3700 REMARK 3 L13: -1.8255 L23: 4.6606 REMARK 3 S TENSOR REMARK 3 S11: 0.5330 S12: 0.4400 S13: -0.3579 REMARK 3 S21: 0.5853 S22: -1.2878 S23: 0.5843 REMARK 3 S31: 1.0817 S32: -2.2605 S33: 0.6572 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'T' AND (RESID 7 THROUGH 16 ) REMARK 3 ORIGIN FOR THE GROUP (A): 32.6226 26.6109 30.7613 REMARK 3 T TENSOR REMARK 3 T11: 1.0995 T22: 0.7855 REMARK 3 T33: 0.7487 T12: 0.1493 REMARK 3 T13: -0.1160 T23: -0.2280 REMARK 3 L TENSOR REMARK 3 L11: 5.2081 L22: 5.8930 REMARK 3 L33: 6.8142 L12: 0.3761 REMARK 3 L13: 0.4323 L23: 2.3997 REMARK 3 S TENSOR REMARK 3 S11: 0.4340 S12: 0.7256 S13: -1.2221 REMARK 3 S21: 0.4695 S22: -0.8188 S23: 0.8321 REMARK 3 S31: 2.1620 S32: -0.3705 S33: 0.4392 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 300 THROUGH 467 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.7337 26.4097 5.8383 REMARK 3 T TENSOR REMARK 3 T11: 0.1840 T22: 0.1549 REMARK 3 T33: 0.1339 T12: -0.0119 REMARK 3 T13: 0.0099 T23: -0.0078 REMARK 3 L TENSOR REMARK 3 L11: 2.4171 L22: 2.4888 REMARK 3 L33: 1.2539 L12: 0.9420 REMARK 3 L13: -0.2900 L23: 0.0593 REMARK 3 S TENSOR REMARK 3 S11: -0.0788 S12: 0.2816 S13: -0.1036 REMARK 3 S21: -0.3027 S22: 0.0871 S23: -0.0425 REMARK 3 S31: 0.0653 S32: -0.0437 S33: -0.0046 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 468 THROUGH 521 ) REMARK 3 ORIGIN FOR THE GROUP (A): 24.2010 44.1497 25.1689 REMARK 3 T TENSOR REMARK 3 T11: 0.2454 T22: 0.1552 REMARK 3 T33: 0.1364 T12: 0.0132 REMARK 3 T13: 0.0388 T23: -0.0622 REMARK 3 L TENSOR REMARK 3 L11: 0.1225 L22: 1.8290 REMARK 3 L33: 1.8992 L12: -0.0681 REMARK 3 L13: -0.1312 L23: -1.0080 REMARK 3 S TENSOR REMARK 3 S11: -0.1562 S12: 0.1987 S13: 0.4642 REMARK 3 S21: 0.1723 S22: -0.1059 S23: -0.1688 REMARK 3 S31: -0.2106 S32: 0.4626 S33: 0.2680 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 522 THROUGH 586 ) REMARK 3 ORIGIN FOR THE GROUP (A): 38.2579 35.1795 46.4525 REMARK 3 T TENSOR REMARK 3 T11: 0.6304 T22: 0.4078 REMARK 3 T33: 0.3126 T12: 0.0114 REMARK 3 T13: -0.0957 T23: -0.0367 REMARK 3 L TENSOR REMARK 3 L11: 3.4848 L22: 4.6736 REMARK 3 L33: 8.6722 L12: 0.1937 REMARK 3 L13: 1.3861 L23: -0.4695 REMARK 3 S TENSOR REMARK 3 S11: 0.2725 S12: 0.1594 S13: -0.2861 REMARK 3 S21: 0.7525 S22: -0.1763 S23: -0.1139 REMARK 3 S31: 0.9447 S32: -0.2377 S33: -0.1130 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 587 THROUGH 676 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.8992 46.8682 28.1562 REMARK 3 T TENSOR REMARK 3 T11: 0.1904 T22: 0.1819 REMARK 3 T33: 0.1771 T12: 0.0025 REMARK 3 T13: -0.0203 T23: -0.0008 REMARK 3 L TENSOR REMARK 3 L11: 2.3392 L22: 0.7258 REMARK 3 L33: 1.8958 L12: -0.6619 REMARK 3 L13: -1.9804 L23: 0.2757 REMARK 3 S TENSOR REMARK 3 S11: -0.0537 S12: -0.1273 S13: 0.1426 REMARK 3 S21: -0.0065 S22: 0.0474 S23: -0.1336 REMARK 3 S31: 0.1405 S32: 0.1827 S33: 0.0143 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 677 THROUGH 743 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.9937 45.0695 53.0249 REMARK 3 T TENSOR REMARK 3 T11: 0.2890 T22: 0.2417 REMARK 3 T33: 0.2174 T12: 0.0010 REMARK 3 T13: -0.0949 T23: 0.0002 REMARK 3 L TENSOR REMARK 3 L11: 5.4408 L22: 4.6515 REMARK 3 L33: 4.3140 L12: -0.9283 REMARK 3 L13: 2.6773 L23: -1.2162 REMARK 3 S TENSOR REMARK 3 S11: 0.3700 S12: -0.3002 S13: -0.3872 REMARK 3 S21: 0.1563 S22: -0.1288 S23: -0.2782 REMARK 3 S31: 0.4339 S32: -0.0056 S33: -0.1707 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 744 THROUGH 876 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.6669 44.0274 30.3356 REMARK 3 T TENSOR REMARK 3 T11: 0.1603 T22: 0.1418 REMARK 3 T33: 0.1389 T12: -0.0029 REMARK 3 T13: 0.0162 T23: -0.0133 REMARK 3 L TENSOR REMARK 3 L11: 1.1619 L22: 2.2801 REMARK 3 L33: 1.2153 L12: 0.6963 REMARK 3 L13: -0.6023 L23: -0.8390 REMARK 3 S TENSOR REMARK 3 S11: 0.0986 S12: -0.0744 S13: 0.0117 REMARK 3 S21: 0.1213 S22: -0.0678 S23: -0.0087 REMARK 3 S31: -0.0430 S32: 0.0003 S33: -0.0328 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 7K5Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-SEP-20. REMARK 100 THE DEPOSITION ID IS D_1000251877. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-SEP-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOXDS REMARK 200 DATA SCALING SOFTWARE : AUTOXDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 59144 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 39.920 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : 0.06529 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.8700 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) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.29920 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: PHASER REMARK 200 STARTING MODEL: 6DSY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50% SATURATED AMMONIUM SULFATE, 0.1M REMARK 280 MES, 2% MPD, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 44.10000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.86200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 46.99400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.86200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 44.10000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 46.99400 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5410 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -55.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: P, T, A 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 DG T 1 REMARK 465 DA T 2 REMARK 465 DC T 3 REMARK 465 ALA A 297 REMARK 465 LYS A 298 REMARK 465 MET A 299 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 ILE A 628 CG1 CG2 CD1 REMARK 470 HIS A 829 CG ND1 CD2 CE1 NE2 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 CB ILE A 628 O2A DTP A 904 1.38 REMARK 500 CB ILE A 628 PA DTP A 904 1.93 REMARK 500 NH1 ARG A 748 O HOH A 1001 2.09 REMARK 500 O HOH A 1219 O HOH A 1333 2.11 REMARK 500 O HOH A 1259 O HOH A 1320 2.11 REMARK 500 O HOH A 1108 O HOH A 1311 2.12 REMARK 500 OP1 DT P 10 N ILE A 628 2.14 REMARK 500 O HOH A 1269 O HOH A 1367 2.14 REMARK 500 NH1 ARG A 637 O HOH A 1002 2.14 REMARK 500 O3 SO4 A 902 O HOH A 1003 2.16 REMARK 500 O HOH A 1347 O HOH A 1369 2.17 REMARK 500 O HOH A 1252 O HOH A 1350 2.17 REMARK 500 O HOH A 1320 O HOH A 1345 2.17 REMARK 500 O HOH A 1182 O HOH A 1245 2.18 REMARK 500 O HOH A 1406 O HOH A 1417 2.18 REMARK 500 O HOH A 1312 O HOH A 1409 2.19 REMARK 500 O HOH A 1283 O HOH A 1370 2.19 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 9 O4' - C4' - C3' ANGL. DEV. = -2.5 DEGREES REMARK 500 DG P 9 O4' - C1' - N9 ANGL. DEV. = 1.9 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 ASP A 402 93.37 -167.01 REMARK 500 ALA A 421 42.52 -87.22 REMARK 500 LEU A 477 -65.36 -126.09 REMARK 500 GLU A 540 -62.32 -99.87 REMARK 500 LEU A 610 -54.62 -125.29 REMARK 500 ARG A 629 -75.40 -80.59 REMARK 500 LEU A 630 -178.84 -67.45 REMARK 500 HIS A 768 20.49 80.12 REMARK 500 HIS A 829 -115.90 56.58 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 A1423 DISTANCE = 6.22 ANGSTROMS REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 DTP A 904 DBREF 7K5Q P 1 10 PDB 7K5Q 7K5Q 1 10 DBREF 7K5Q T 1 16 PDB 7K5Q 7K5Q 1 16 DBREF 7K5Q A 297 876 UNP E1C9K5 E1C9K5_GEOSE 1 580 SEQADV 7K5Q THR A 550 UNP E1C9K5 SER 254 VARIANT SEQRES 1 P 10 DG DC DG DA DT DC DA DC DG DT SEQRES 1 T 16 DG DA DC DG DT DA DC DG DT DG DA DT DC SEQRES 2 T 16 DG DC DA SEQRES 1 A 580 ALA LYS MET ALA PHE THR LEU ALA ASP ARG VAL THR GLU SEQRES 2 A 580 GLU MET LEU ALA ASP LYS ALA ALA LEU VAL VAL GLU VAL SEQRES 3 A 580 VAL GLU GLU ASN TYR HIS ASP ALA PRO ILE VAL GLY ILE SEQRES 4 A 580 ALA VAL VAL ASN GLU HIS GLY ARG PHE PHE LEU ARG PRO SEQRES 5 A 580 GLU THR ALA LEU ALA ASP PRO GLN PHE VAL ALA TRP LEU SEQRES 6 A 580 GLY ASP GLU THR LYS LYS LYS SER MET PHE ASP SER LYS SEQRES 7 A 580 ARG ALA ALA VAL ALA LEU LYS TRP LYS GLY ILE GLU LEU SEQRES 8 A 580 CYS GLY VAL SER PHE ASP LEU LEU LEU ALA ALA TYR LEU SEQRES 9 A 580 LEU ASP PRO ALA GLN GLY VAL ASP ASP VAL ALA ALA ALA SEQRES 10 A 580 ALA LYS MET LYS GLN TYR GLU ALA VAL ARG PRO ASP GLU SEQRES 11 A 580 ALA VAL TYR GLY LYS GLY ALA LYS ARG ALA VAL PRO ASP SEQRES 12 A 580 GLU PRO VAL LEU ALA GLU HIS LEU VAL ARG LYS ALA ALA SEQRES 13 A 580 ALA ILE TRP ALA LEU GLU ARG PRO PHE LEU ASP GLU LEU SEQRES 14 A 580 ARG ARG ASN GLU GLN ASP ARG LEU LEU VAL GLU LEU GLU SEQRES 15 A 580 GLN PRO LEU SER SER ILE LEU ALA GLU MET GLU PHE ALA SEQRES 16 A 580 GLY VAL LYS VAL ASP THR LYS ARG LEU GLU GLN MET GLY SEQRES 17 A 580 GLU GLU LEU ALA GLU GLN LEU ARG THR VAL GLU GLN ARG SEQRES 18 A 580 ILE TYR GLU LEU ALA GLY GLN GLU PHE ASN ILE ASN SER SEQRES 19 A 580 PRO LYS GLN LEU GLY VAL ILE LEU PHE GLU LYS LEU GLN SEQRES 20 A 580 LEU PRO VAL LEU LYS LYS THR LYS THR GLY TYR SER THR SEQRES 21 A 580 SER ALA ASP VAL LEU GLU LYS LEU ALA PRO TYR HIS GLU SEQRES 22 A 580 ILE VAL GLU ASN ILE LEU HIS TYR ARG GLN LEU GLY LYS SEQRES 23 A 580 LEU GLN SER THR TYR ILE GLU GLY LEU LEU LYS VAL VAL SEQRES 24 A 580 ARG PRO ASP THR LYS LYS VAL HIS THR ILE PHE ASN GLN SEQRES 25 A 580 ALA LEU THR GLN THR GLY ARG LEU SER SER THR GLU PRO SEQRES 26 A 580 ASN LEU GLN ASN ILE PRO ILE ARG LEU GLU GLU GLY ARG SEQRES 27 A 580 LYS ILE ARG GLN ALA PHE VAL PRO SER GLU SER ASP TRP SEQRES 28 A 580 LEU ILE PHE ALA ALA ASP TYR SER GLN ILE GLU LEU ARG SEQRES 29 A 580 VAL LEU ALA HIS ILE ALA GLU ASP ASP ASN LEU MET GLU SEQRES 30 A 580 ALA PHE ARG ARG ASP LEU ASP ILE HIS THR LYS THR ALA SEQRES 31 A 580 MET ASP ILE PHE GLN VAL SER GLU ASP GLU VAL THR PRO SEQRES 32 A 580 ASN MET ARG ARG GLN ALA LYS ALA VAL ASN PHE GLY ILE SEQRES 33 A 580 VAL TYR GLY ILE SER ASP TYR GLY LEU ALA GLN ASN LEU SEQRES 34 A 580 ASN ILE SER ARG LYS GLU ALA ALA GLU PHE ILE GLU ARG SEQRES 35 A 580 TYR PHE GLU SER PHE PRO GLY VAL LYS ARG TYR MET GLU SEQRES 36 A 580 ASN ILE VAL GLN GLU ALA LYS GLN LYS GLY TYR VAL THR SEQRES 37 A 580 THR LEU LEU HIS ARG ARG ARG TYR LEU PRO ASP ILE THR SEQRES 38 A 580 SER ARG ASN PHE ASN VAL ARG SER PHE ALA GLU ARG MET SEQRES 39 A 580 ALA MET ASN THR PRO ILE GLN GLY SER ALA ALA ASP ILE SEQRES 40 A 580 ILE LYS LYS ALA MET ILE ASP LEU ASN ALA ARG LEU LYS SEQRES 41 A 580 GLU GLU ARG LEU GLN ALA ARG LEU LEU LEU GLN VAL HIS SEQRES 42 A 580 ASP GLU LEU ILE LEU GLU ALA PRO LYS GLU GLU MET GLU SEQRES 43 A 580 ARG LEU CYS ARG LEU VAL PRO GLU VAL MET GLU GLN ALA SEQRES 44 A 580 VAL THR LEU ARG VAL PRO LEU LYS VAL ASP TYR HIS TYR SEQRES 45 A 580 GLY SER THR TRP TYR ASP ALA LYS HET SO4 A 901 5 HET SO4 A 902 5 HET SO4 A 903 5 HET DTP A 904 21 HETNAM SO4 SULFATE ION HETNAM DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE FORMUL 4 SO4 3(O4 S 2-) FORMUL 7 DTP C10 H16 N5 O12 P3 FORMUL 8 HOH *439(H2 O) HELIX 1 AA1 THR A 308 ALA A 313 5 6 HELIX 2 AA2 ARG A 347 LEU A 352 1 6 HELIX 3 AA3 ASP A 354 ASP A 363 1 10 HELIX 4 AA4 ASP A 372 TRP A 382 1 11 HELIX 5 AA5 LEU A 394 ASP A 402 1 9 HELIX 6 AA6 PRO A 403 GLY A 406 5 4 HELIX 7 AA7 ASP A 409 MET A 416 1 8 HELIX 8 AA8 PRO A 424 GLY A 430 1 7 HELIX 9 AA9 LYS A 431 ARG A 435 5 5 HELIX 10 AB1 ASP A 439 ASN A 468 1 30 HELIX 11 AB2 GLN A 470 LEU A 477 1 8 HELIX 12 AB3 LEU A 477 GLY A 492 1 16 HELIX 13 AB4 ASP A 496 GLY A 523 1 28 HELIX 14 AB5 SER A 530 PHE A 539 1 10 HELIX 15 AB6 SER A 557 ALA A 565 1 9 HELIX 16 AB7 PRO A 566 HIS A 568 5 3 HELIX 17 AB8 GLU A 569 TYR A 587 1 19 HELIX 18 AB9 TYR A 587 VAL A 595 1 9 HELIX 19 AC1 LEU A 630 LYS A 635 1 6 HELIX 20 AC2 ILE A 636 GLN A 638 5 3 HELIX 21 AC3 GLN A 656 GLU A 667 1 12 HELIX 22 AC4 ASP A 668 ARG A 677 1 10 HELIX 23 AC5 ASP A 680 GLN A 691 1 12 HELIX 24 AC6 SER A 693 VAL A 697 5 5 HELIX 25 AC7 THR A 698 GLY A 715 1 18 HELIX 26 AC8 SER A 717 ASN A 726 1 10 HELIX 27 AC9 SER A 728 PHE A 743 1 16 HELIX 28 AD1 PHE A 743 GLY A 761 1 19 HELIX 29 AD2 PRO A 774 SER A 778 5 5 HELIX 30 AD3 ASN A 780 GLU A 818 1 39 HELIX 31 AD4 GLU A 840 GLN A 854 1 15 SHEET 1 AA1 6 THR A 302 LEU A 303 0 SHEET 2 AA1 6 GLY A 342 LEU A 346 1 O ARG A 343 N THR A 302 SHEET 3 AA1 6 GLY A 334 ASN A 339 -1 N ILE A 335 O LEU A 346 SHEET 4 AA1 6 LYS A 315 GLU A 321 -1 N ALA A 317 O VAL A 338 SHEET 5 AA1 6 LYS A 367 MET A 370 1 O SER A 369 N LEU A 318 SHEET 6 AA1 6 VAL A 390 ASP A 393 1 O PHE A 392 N MET A 370 SHEET 1 AA2 3 LYS A 601 VAL A 602 0 SHEET 2 AA2 3 VAL A 493 VAL A 495 -1 N VAL A 493 O VAL A 602 SHEET 3 AA2 3 PHE A 640 VAL A 641 -1 O VAL A 641 N LYS A 494 SHEET 1 AA3 2 ILE A 605 ASN A 607 0 SHEET 2 AA3 2 SER A 617 THR A 619 -1 O SER A 617 N ASN A 607 SHEET 1 AA4 4 ARG A 823 VAL A 828 0 SHEET 2 AA4 4 GLU A 831 PRO A 837 -1 O ILE A 833 N LEU A 825 SHEET 3 AA4 4 TRP A 647 TYR A 654 -1 N PHE A 650 O LEU A 834 SHEET 4 AA4 4 VAL A 864 GLY A 869 -1 O ASP A 865 N ASP A 653 SHEET 1 AA5 2 TYR A 762 THR A 764 0 SHEET 2 AA5 2 ARG A 770 TYR A 772 -1 O ARG A 771 N VAL A 763 CISPEP 1 GLU A 620 PRO A 621 0 2.48 CRYST1 88.200 93.988 105.724 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 0.011338 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010640 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009459 0.00000