PDB Short entry for 6DSV HEADER TRANSFERASE/DNA 14-JUN-18 6DSV TITLE BST DNA POLYMERASE I POST-CHEMISTRY (N+2) STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*GP*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 POLYMERASE I; COMPND 7 CHAIN: A; COMPND 8 EC: 2.7.7.7; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: DNA (5'-D(P*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-3'); COMPND 12 CHAIN: T; COMPND 13 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 ORGANISM_SCIENTIFIC: GEOBACILLUS STEAROTHERMOPHILUS; SOURCE 7 ORGANISM_TAXID: 1422; SOURCE 8 GENE: POLA; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630 KEYWDS DNA SYNTHESIS, TRANSFERASE, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.CHIM,L.N.JACKSON,J.C.CHAPUT REVDAT 3 13-MAR-24 6DSV 1 REMARK REVDAT 2 27-NOV-19 6DSV 1 REMARK REVDAT 1 31-OCT-18 6DSV 0 JRNL AUTH N.CHIM,L.N.JACKSON,A.M.TRINH,J.C.CHAPUT JRNL TITL CRYSTAL STRUCTURES OF DNA POLYMERASE I CAPTURE NOVEL JRNL TITL 2 INTERMEDIATES IN THE DNA SYNTHESIS PATHWAY. JRNL REF ELIFE V. 7 2018 JRNL REFN ESSN 2050-084X JRNL PMID 30338759 JRNL DOI 10.7554/ELIFE.40444 REMARK 2 REMARK 2 RESOLUTION. 1.99 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.54 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 58991 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.400 REMARK 3 FREE R VALUE TEST SET COUNT : 2003 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 43.5514 - 4.7942 0.99 4297 153 0.1904 0.1934 REMARK 3 2 4.7942 - 3.8060 1.00 4151 144 0.1560 0.1800 REMARK 3 3 3.8060 - 3.3251 1.00 4095 145 0.1664 0.1982 REMARK 3 4 3.3251 - 3.0212 1.00 4081 145 0.1774 0.2197 REMARK 3 5 3.0212 - 2.8047 1.00 4079 144 0.1872 0.2374 REMARK 3 6 2.8047 - 2.6393 1.00 4051 138 0.1993 0.2774 REMARK 3 7 2.6393 - 2.5072 1.00 4046 148 0.1943 0.2182 REMARK 3 8 2.5072 - 2.3980 1.00 4040 145 0.1951 0.2568 REMARK 3 9 2.3980 - 2.3057 1.00 4050 133 0.1969 0.2665 REMARK 3 10 2.3057 - 2.2262 1.00 3995 150 0.2048 0.2509 REMARK 3 11 2.2262 - 2.1566 1.00 4039 134 0.2156 0.2500 REMARK 3 12 2.1566 - 2.0949 1.00 4008 137 0.2329 0.2525 REMARK 3 13 2.0949 - 2.0398 1.00 4039 149 0.2560 0.3225 REMARK 3 14 2.0398 - 1.9900 1.00 4017 138 0.3571 0.4066 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.330 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) : 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 5203 REMARK 3 ANGLE : 0.844 7137 REMARK 3 CHIRALITY : 0.050 807 REMARK 3 PLANARITY : 0.005 848 REMARK 3 DIHEDRAL : 10.222 3091 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'P' AND (RESID 1 THROUGH 10 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.8763 28.0916 33.0822 REMARK 3 T TENSOR REMARK 3 T11: 0.8128 T22: 0.9142 REMARK 3 T33: 0.4724 T12: 0.0905 REMARK 3 T13: -0.1478 T23: -0.1631 REMARK 3 L TENSOR REMARK 3 L11: 3.3772 L22: 4.5797 REMARK 3 L33: 8.1404 L12: 1.7768 REMARK 3 L13: -2.4900 L23: 3.4818 REMARK 3 S TENSOR REMARK 3 S11: 0.3025 S12: 1.1101 S13: -0.6645 REMARK 3 S21: -0.2891 S22: -0.5654 S23: 0.4347 REMARK 3 S31: 1.4651 S32: -1.1578 S33: 0.1971 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'P' AND (RESID 11 THROUGH 11 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.4475 42.2356 36.9444 REMARK 3 T TENSOR REMARK 3 T11: 1.2925 T22: 0.9037 REMARK 3 T33: 1.7237 T12: 0.4045 REMARK 3 T13: 0.6295 T23: 0.3373 REMARK 3 L TENSOR REMARK 3 L11: 8.7463 L22: 2.6868 REMARK 3 L33: 2.6502 L12: 2.7118 REMARK 3 L13: 0.7091 L23: 2.2414 REMARK 3 S TENSOR REMARK 3 S11: -0.0941 S12: -0.3836 S13: -0.2871 REMARK 3 S21: -0.0268 S22: 0.0198 S23: 0.2753 REMARK 3 S31: 0.1114 S32: -0.0607 S33: 0.0688 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 300 THROUGH 467 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.5638 26.1246 5.6316 REMARK 3 T TENSOR REMARK 3 T11: 0.1671 T22: 0.1422 REMARK 3 T33: 0.1516 T12: -0.0204 REMARK 3 T13: 0.0203 T23: -0.0087 REMARK 3 L TENSOR REMARK 3 L11: 2.0959 L22: 2.2677 REMARK 3 L33: 1.6758 L12: 0.5966 REMARK 3 L13: -0.2603 L23: 0.1128 REMARK 3 S TENSOR REMARK 3 S11: -0.1125 S12: 0.2494 S13: -0.1358 REMARK 3 S21: -0.3425 S22: 0.0986 S23: -0.0718 REMARK 3 S31: 0.1293 S32: 0.0190 S33: 0.0018 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 468 THROUGH 646 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.4746 40.8265 31.8948 REMARK 3 T TENSOR REMARK 3 T11: 0.2767 T22: 0.2344 REMARK 3 T33: 0.2001 T12: 0.0350 REMARK 3 T13: -0.0012 T23: 0.0023 REMARK 3 L TENSOR REMARK 3 L11: 1.0820 L22: 0.7898 REMARK 3 L33: 1.7743 L12: -0.1467 REMARK 3 L13: 0.8137 L23: -0.0990 REMARK 3 S TENSOR REMARK 3 S11: -0.0251 S12: -0.0281 S13: 0.1520 REMARK 3 S21: 0.2511 S22: -0.0491 S23: -0.1699 REMARK 3 S31: 0.0627 S32: 0.3452 S33: 0.0559 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 647 THROUGH 876 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.5000 44.6775 37.3203 REMARK 3 T TENSOR REMARK 3 T11: 0.1467 T22: 0.1304 REMARK 3 T33: 0.1628 T12: 0.0041 REMARK 3 T13: -0.0095 T23: 0.0006 REMARK 3 L TENSOR REMARK 3 L11: 0.7187 L22: 1.3677 REMARK 3 L33: 0.8722 L12: 0.2222 REMARK 3 L13: -0.0856 L23: 0.0114 REMARK 3 S TENSOR REMARK 3 S11: 0.0366 S12: -0.0852 S13: 0.0153 REMARK 3 S21: 0.1723 S22: -0.0219 S23: -0.1501 REMARK 3 S31: -0.0015 S32: -0.0415 S33: -0.0072 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'T' AND (RESID 4 THROUGH 15 ) REMARK 3 ORIGIN FOR THE GROUP (A): 29.2735 27.2021 32.0348 REMARK 3 T TENSOR REMARK 3 T11: 1.0070 T22: 0.9076 REMARK 3 T33: 0.6636 T12: 0.0715 REMARK 3 T13: 0.0779 T23: -0.2423 REMARK 3 L TENSOR REMARK 3 L11: 6.7778 L22: 3.5521 REMARK 3 L33: 5.2052 L12: 0.5614 REMARK 3 L13: -0.9028 L23: 2.2226 REMARK 3 S TENSOR REMARK 3 S11: 0.0783 S12: 0.8295 S13: -1.1507 REMARK 3 S21: 1.1463 S22: -0.5118 S23: 0.7993 REMARK 3 S31: 2.0062 S32: -0.8021 S33: 0.4330 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 6DSV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1000234747. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-FEB-18 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 : 58993 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.990 REMARK 200 RESOLUTION RANGE LOW (A) : 44.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : 0.32700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.7500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.99 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.06 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.74500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.90 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 43.54100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.36800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 46.53450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.36800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 43.54100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 46.53450 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: 4370 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -47.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: P, A, 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ALA A 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 GLU A 364 CG CD OE1 OE2 REMARK 470 GLU A 386 CG CD OE1 OE2 REMARK 470 GLU A 426 CG CD OE1 OE2 REMARK 470 LYS A 431 CG CD CE NZ REMARK 470 LYS A 549 CG CD CE NZ REMARK 470 ARG A 629 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 630 CG CD1 CD2 REMARK 470 LYS A 730 CG CD CE NZ 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 OE1 GLU A 658 MG MG A 901 1.66 REMARK 500 C6 DA P 11 O4 DT T 4 1.85 REMARK 500 N7 DA P 11 O4 DT T 4 2.00 REMARK 500 C5 DA P 11 O4 DT T 4 2.00 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 DA P 11 C1' - O4' - C4' ANGL. DEV. = -9.2 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 372 60.02 63.49 REMARK 500 ASP A 402 93.40 -164.80 REMARK 500 ALA A 421 37.01 -87.55 REMARK 500 ILE A 628 -37.56 -143.72 REMARK 500 HIS A 829 -104.95 50.67 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 902 DBREF 6DSV P 1 11 PDB 6DSV 6DSV 1 11 DBREF 6DSV A 297 876 UNP E1C9K5 E1C9K5_GEOSE 1 580 DBREF 6DSV T 4 15 PDB 6DSV 6DSV 4 15 SEQADV 6DSV THR A 550 UNP E1C9K5 SER 254 CONFLICT SEQRES 1 P 11 DG DC DG DA DT DC DA DC DG DT 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 SEQRES 1 T 12 DT DA DC DG DT DG DA DT DC DG DC DA HET MG A 901 1 HET SO4 A 902 5 HETNAM MG MAGNESIUM ION HETNAM SO4 SULFATE ION FORMUL 4 MG MG 2+ FORMUL 5 SO4 O4 S 2- FORMUL 6 HOH *384(H2 O) HELIX 1 AA1 THR A 308 LEU A 312 5 5 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 ALA A 522 1 27 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 GLY A 715 1 18 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 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 VAL A 337 O PHE A 344 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 GLU A 831 N VAL A 828 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 HIS A 867 N ALA A 651 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 LINK N6 DA P 11 O4 DT T 4 1555 1555 1.42 LINK OD1 ASP A 830 MG MG A 901 1555 1555 1.81 CISPEP 1 GLU A 620 PRO A 621 0 0.22 SITE 1 AC1 2 GLU A 658 ASP A 830 SITE 1 AC2 3 ARG A 702 LYS A 706 HOH A1102 CRYST1 87.082 93.069 104.736 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 0.011483 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010745 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009548 0.00000