HEADER TRANSFERASE/DNA 17-SEP-20 7K5T TITLE BST DNA POLYMERASE I TIME-RESOLVED STRUCTURE, 25.5 HR POST DATP AND TITLE 2 DCTP ADDITION COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(P*CP*GP*AP*TP*CP*AP*CP*GP*TP*A)-3'); COMPND 3 CHAIN: P; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(P*CP*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*C)-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 7K5T 1 REMARK REVDAT 2 19-MAY-21 7K5T 1 JRNL REVDAT 1 03-MAR-21 7K5T 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. 2.30 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.79 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 38713 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.620 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 46.7900 - 5.4100 1.00 3028 141 0.1888 0.2244 REMARK 3 2 5.4100 - 4.2900 1.00 2885 147 0.1543 0.1861 REMARK 3 3 4.2900 - 3.7500 1.00 2862 140 0.1626 0.1813 REMARK 3 4 3.7500 - 3.4100 0.99 2816 142 0.1868 0.2524 REMARK 3 5 3.4100 - 3.1600 1.00 2856 130 0.2047 0.2515 REMARK 3 6 3.1600 - 2.9800 1.00 2797 145 0.2193 0.3034 REMARK 3 7 2.9800 - 2.8300 1.00 2831 132 0.2216 0.2653 REMARK 3 8 2.8300 - 2.7000 1.00 2798 148 0.2100 0.2723 REMARK 3 9 2.7000 - 2.6000 1.00 2824 127 0.2152 0.3014 REMARK 3 10 2.6000 - 2.5100 1.00 2794 137 0.2132 0.2686 REMARK 3 11 2.5100 - 2.4300 1.00 2813 142 0.2212 0.2953 REMARK 3 12 2.4300 - 2.3600 1.00 2782 145 0.2309 0.2899 REMARK 3 13 2.3600 - 2.3000 1.00 2837 114 0.2439 0.3199 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) : 0.286 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.736 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 40.57 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 57.51 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 5274 REMARK 3 ANGLE : 0.881 7227 REMARK 3 CHIRALITY : 0.050 813 REMARK 3 PLANARITY : 0.005 855 REMARK 3 DIHEDRAL : 10.335 3136 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 2 THROUGH 11 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.9542 28.3919 33.0735 REMARK 3 T TENSOR REMARK 3 T11: 1.1051 T22: 1.0928 REMARK 3 T33: 0.8410 T12: 0.0750 REMARK 3 T13: -0.0113 T23: -0.2397 REMARK 3 L TENSOR REMARK 3 L11: 1.8023 L22: 3.8583 REMARK 3 L33: 4.0762 L12: -0.0916 REMARK 3 L13: -1.3991 L23: 2.9741 REMARK 3 S TENSOR REMARK 3 S11: 0.5789 S12: 1.0635 S13: -0.3242 REMARK 3 S21: -0.1489 S22: -1.3740 S23: 0.0305 REMARK 3 S31: 0.6422 S32: -1.5623 S33: 0.7828 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'T' AND (RESID 3 THROUGH 15 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.1244 27.7920 32.9180 REMARK 3 T TENSOR REMARK 3 T11: 1.3103 T22: 0.9282 REMARK 3 T33: 1.0013 T12: 0.0556 REMARK 3 T13: 0.0671 T23: -0.2136 REMARK 3 L TENSOR REMARK 3 L11: 3.2440 L22: 2.5676 REMARK 3 L33: 2.5694 L12: 0.0018 REMARK 3 L13: 0.8918 L23: -0.4841 REMARK 3 S TENSOR REMARK 3 S11: 0.2489 S12: 0.2552 S13: -0.7873 REMARK 3 S21: 0.6973 S22: -0.5495 S23: 0.9560 REMARK 3 S31: 1.7957 S32: -0.6026 S33: 0.4344 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 300 THROUGH 439 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.0497 27.4392 5.1880 REMARK 3 T TENSOR REMARK 3 T11: 0.3564 T22: 0.2892 REMARK 3 T33: 0.2510 T12: -0.0059 REMARK 3 T13: 0.0093 T23: -0.0169 REMARK 3 L TENSOR REMARK 3 L11: 2.2839 L22: 2.1551 REMARK 3 L33: 1.1975 L12: 0.7720 REMARK 3 L13: -0.0252 L23: 0.1492 REMARK 3 S TENSOR REMARK 3 S11: -0.0665 S12: 0.2487 S13: -0.0594 REMARK 3 S21: -0.4310 S22: 0.0837 S23: -0.0203 REMARK 3 S31: 0.0471 S32: 0.0332 S33: -0.0099 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 440 THROUGH 522 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.3842 36.1299 19.8063 REMARK 3 T TENSOR REMARK 3 T11: 0.2988 T22: 0.2593 REMARK 3 T33: 0.2979 T12: 0.0133 REMARK 3 T13: 0.0152 T23: 0.0168 REMARK 3 L TENSOR REMARK 3 L11: 0.8001 L22: 0.8852 REMARK 3 L33: 1.2993 L12: 0.0503 REMARK 3 L13: 0.2028 L23: 0.0166 REMARK 3 S TENSOR REMARK 3 S11: -0.0376 S12: 0.0153 S13: -0.0064 REMARK 3 S21: 0.0082 S22: -0.0404 S23: -0.1077 REMARK 3 S31: 0.0011 S32: 0.1434 S33: 0.0652 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 523 THROUGH 604 ) REMARK 3 ORIGIN FOR THE GROUP (A): 35.6435 37.1551 40.1153 REMARK 3 T TENSOR REMARK 3 T11: 0.6249 T22: 0.4697 REMARK 3 T33: 0.4470 T12: 0.0328 REMARK 3 T13: -0.0277 T23: -0.0165 REMARK 3 L TENSOR REMARK 3 L11: 0.6511 L22: 0.9735 REMARK 3 L33: 2.6330 L12: 0.0211 REMARK 3 L13: 1.2365 L23: 0.0654 REMARK 3 S TENSOR REMARK 3 S11: 0.1404 S12: 0.0024 S13: -0.0064 REMARK 3 S21: 0.3433 S22: 0.0176 S23: -0.1517 REMARK 3 S31: 0.5659 S32: 0.0900 S33: -0.1321 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 605 THROUGH 646 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.1944 45.4857 26.2188 REMARK 3 T TENSOR REMARK 3 T11: 0.4419 T22: 0.3459 REMARK 3 T33: 0.3909 T12: 0.0335 REMARK 3 T13: 0.0404 T23: 0.0065 REMARK 3 L TENSOR REMARK 3 L11: 1.3670 L22: 2.3615 REMARK 3 L33: 0.6369 L12: 0.5157 REMARK 3 L13: -0.5225 L23: -0.0169 REMARK 3 S TENSOR REMARK 3 S11: 0.0952 S12: -0.1315 S13: 0.1527 REMARK 3 S21: 0.4424 S22: 0.0982 S23: -0.0566 REMARK 3 S31: -0.2350 S32: 0.0657 S33: -0.2370 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 647 THROUGH 728 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.7035 47.9589 46.1152 REMARK 3 T TENSOR REMARK 3 T11: 0.3426 T22: 0.3082 REMARK 3 T33: 0.3439 T12: 0.0050 REMARK 3 T13: -0.0491 T23: -0.0047 REMARK 3 L TENSOR REMARK 3 L11: 0.5903 L22: 1.2149 REMARK 3 L33: 1.9354 L12: 0.4003 REMARK 3 L13: -0.1688 L23: 0.0331 REMARK 3 S TENSOR REMARK 3 S11: 0.0240 S12: -0.1360 S13: -0.0567 REMARK 3 S21: 0.2569 S22: -0.0269 S23: -0.1678 REMARK 3 S31: 0.0349 S32: 0.0471 S33: -0.0127 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 729 THROUGH 876 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.5813 43.2543 33.1636 REMARK 3 T TENSOR REMARK 3 T11: 0.3103 T22: 0.2890 REMARK 3 T33: 0.3189 T12: 0.0052 REMARK 3 T13: -0.0149 T23: -0.0134 REMARK 3 L TENSOR REMARK 3 L11: 0.7863 L22: 1.4559 REMARK 3 L33: 1.1548 L12: 0.4633 REMARK 3 L13: -0.3045 L23: -0.3284 REMARK 3 S TENSOR REMARK 3 S11: 0.1008 S12: -0.0532 S13: -0.0064 REMARK 3 S21: 0.2951 S22: -0.0507 S23: -0.0165 REMARK 3 S31: -0.1468 S32: -0.0709 S33: -0.0266 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 7K5T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-SEP-20. REMARK 100 THE DEPOSITION ID IS D_1000251880. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JUL-20 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 : 5.0.2 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 : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOXDS REMARK 200 DATA SCALING SOFTWARE : AUTOXDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38768 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 46.790 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.06221 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.2300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.48010 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 (%): 57.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50% AMMONIUM SULFATE, 0.1M MES, 2% REMARK 280 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 43.31550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.73550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 46.79450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.73550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 43.31550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 46.79450 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: 28010 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 P 1 REMARK 465 DG T 1 REMARK 465 DA T 2 REMARK 465 DA T 16 REMARK 465 ALA A 297 REMARK 465 LYS A 298 REMARK 465 MET A 299 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 ND1 HIS A 829 O2 DCP A 904 1.30 REMARK 500 CE1 HIS A 829 O2 DCP A 904 2.03 REMARK 500 CG HIS A 829 O2 DCP A 904 2.04 REMARK 500 O HOH A 1098 O HOH A 1110 2.07 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 DA P 11 O3' DA P 11 C3' -0.039 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 DT P 10 O4' - C1' - N1 ANGL. DEV. = 2.1 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 97.11 -162.00 REMARK 500 ALA A 421 40.20 -85.23 REMARK 500 GLN A 524 145.57 -176.40 REMARK 500 LEU A 610 -59.67 -123.25 REMARK 500 ILE A 628 -36.52 -144.17 REMARK 500 ASN A 726 65.55 37.18 REMARK 500 HIS A 768 18.77 80.55 REMARK 500 HIS A 829 -103.56 47.90 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 A1115 DISTANCE = 6.03 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 DCP A 904 DBREF 7K5T P 1 11 PDB 7K5T 7K5T 1 11 DBREF 7K5T T 1 16 PDB 7K5T 7K5T 1 16 DBREF 7K5T A 297 876 UNP E1C9K5 E1C9K5_GEOSE 1 580 SEQADV 7K5T THR A 550 UNP E1C9K5 SER 254 VARIANT SEQRES 1 P 11 DG DC DG DA DT DC DA DC DG DT DA 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 DCP A 904 16 HETNAM SO4 SULFATE ION HETNAM DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE FORMUL 4 SO4 3(O4 S 2-) FORMUL 7 DCP C9 H16 N3 O13 P3 FORMUL 8 HOH *120(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 GLU A 540 1 11 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 ASN A 622 ILE A 626 5 5 HELIX 20 AC2 LEU A 630 LYS A 635 1 6 HELIX 21 AC3 ILE A 636 GLN A 638 5 3 HELIX 22 AC4 GLN A 656 GLU A 667 1 12 HELIX 23 AC5 ASP A 668 ARG A 677 1 10 HELIX 24 AC6 ASP A 680 GLN A 691 1 12 HELIX 25 AC7 SER A 693 VAL A 697 5 5 HELIX 26 AC8 THR A 698 TYR A 714 1 17 HELIX 27 AC9 SER A 717 ASN A 726 1 10 HELIX 28 AD1 SER A 728 PHE A 743 1 16 HELIX 29 AD2 PHE A 743 GLY A 761 1 19 HELIX 30 AD3 PRO A 774 SER A 778 5 5 HELIX 31 AD4 ASN A 780 GLU A 818 1 39 HELIX 32 AD5 GLU A 840 ALA A 855 1 16 SHEET 1 AA1 6 THR A 302 ALA A 304 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 THR A 619 N ILE A 605 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 826 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 -1.01 CRYST1 86.631 93.589 105.471 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 0.011543 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010685 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009481 0.00000