HEADER TRANSFERASE/DNA 14-JUN-18 6DSU
TITLE BST DNA POLYMERASE I PRE-INSERTION COMPLEX STRUCTURE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA (5'-D(*GP*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*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 EC: 2.7.7.7;
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 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 SYNTHESIS, TRANSFERASE, TRANSFERASE-DNA COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR N.CHIM,L.N.JACKSON,J.C.CHAPUT
REVDAT 3 13-MAR-24 6DSU 1 REMARK
REVDAT 2 27-NOV-19 6DSU 1 REMARK
REVDAT 1 31-OCT-18 6DSU 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. 1.98 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 : ML
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.98
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.69
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340
REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7
REMARK 3 NUMBER OF REFLECTIONS : 59667
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.223
REMARK 3 R VALUE (WORKING SET) : 0.222
REMARK 3 FREE R VALUE : 0.272
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.320
REMARK 3 FREE R VALUE TEST SET COUNT : 1386
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 46.7060 - 4.2648 0.96 5933 143 0.1789 0.2206
REMARK 3 2 4.2648 - 3.3854 1.00 5970 142 0.1772 0.2162
REMARK 3 3 3.3854 - 2.9576 1.00 5919 143 0.2066 0.2668
REMARK 3 4 2.9576 - 2.6872 1.00 5882 134 0.2171 0.2740
REMARK 3 5 2.6872 - 2.4946 1.00 5861 142 0.2252 0.2581
REMARK 3 6 2.4946 - 2.3475 1.00 5862 141 0.2426 0.2763
REMARK 3 7 2.3475 - 2.2300 0.97 5642 137 0.3663 0.4579
REMARK 3 8 2.2300 - 2.1329 0.96 5625 139 0.3793 0.4448
REMARK 3 9 2.1329 - 2.0508 0.99 5830 121 0.2369 0.2649
REMARK 3 10 2.0508 - 1.9800 0.99 5757 144 0.2255 0.2818
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) : 0.200
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.050
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 : 0.003 5272
REMARK 3 ANGLE : 0.602 7224
REMARK 3 CHIRALITY : 0.042 807
REMARK 3 PLANARITY : 0.004 858
REMARK 3 DIHEDRAL : 17.317 3130
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 468 THROUGH 630 )
REMARK 3 ORIGIN FOR THE GROUP (A): 28.9129 39.6598 32.7222
REMARK 3 T TENSOR
REMARK 3 T11: 0.3574 T22: 0.2726
REMARK 3 T33: 0.2166 T12: 0.0036
REMARK 3 T13: -0.0483 T23: 0.0236
REMARK 3 L TENSOR
REMARK 3 L11: 1.3312 L22: 1.0573
REMARK 3 L33: 2.0904 L12: -0.2049
REMARK 3 L13: 1.2364 L23: -0.1264
REMARK 3 S TENSOR
REMARK 3 S11: 0.0225 S12: -0.1222 S13: 0.0456
REMARK 3 S21: 0.4310 S22: -0.0749 S23: -0.2642
REMARK 3 S31: 0.0707 S32: 0.3357 S33: 0.0481
REMARK 3 TLS GROUP : 2
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 631 THROUGH 876 )
REMARK 3 ORIGIN FOR THE GROUP (A): 6.8300 45.1236 36.8091
REMARK 3 T TENSOR
REMARK 3 T11: 0.1015 T22: 0.1059
REMARK 3 T33: 0.1404 T12: 0.0063
REMARK 3 T13: -0.0224 T23: -0.0041
REMARK 3 L TENSOR
REMARK 3 L11: 1.0104 L22: 1.3187
REMARK 3 L33: 1.1526 L12: 0.1876
REMARK 3 L13: -0.2853 L23: 0.0893
REMARK 3 S TENSOR
REMARK 3 S11: 0.0458 S12: -0.0966 S13: -0.0123
REMARK 3 S21: 0.1989 S22: -0.0218 S23: -0.2042
REMARK 3 S31: 0.0139 S32: 0.0073 S33: -0.0004
REMARK 3 TLS GROUP : 3
REMARK 3 SELECTION: CHAIN 'P' AND (RESID 1 THROUGH 10 )
REMARK 3 ORIGIN FOR THE GROUP (A): 27.2035 30.6750 34.4803
REMARK 3 T TENSOR
REMARK 3 T11: 0.5906 T22: 0.7666
REMARK 3 T33: 0.3926 T12: 0.0465
REMARK 3 T13: -0.0878 T23: -0.1185
REMARK 3 L TENSOR
REMARK 3 L11: 4.9730 L22: 8.7519
REMARK 3 L33: 7.2794 L12: 0.9991
REMARK 3 L13: -0.7955 L23: 3.1464
REMARK 3 S TENSOR
REMARK 3 S11: 0.3568 S12: 0.4623 S13: -0.1706
REMARK 3 S21: 0.3600 S22: -0.7555 S23: 0.6839
REMARK 3 S31: 0.7200 S32: -0.9791 S33: 0.4107
REMARK 3 TLS GROUP : 4
REMARK 3 SELECTION: CHAIN 'T' AND (RESID 4 THROUGH 14 )
REMARK 3 ORIGIN FOR THE GROUP (A): 28.6910 28.9788 32.1223
REMARK 3 T TENSOR
REMARK 3 T11: 0.8267 T22: 0.6605
REMARK 3 T33: 0.6209 T12: 0.0831
REMARK 3 T13: 0.0160 T23: -0.1286
REMARK 3 L TENSOR
REMARK 3 L11: 2.0106 L22: 8.4643
REMARK 3 L33: 7.4420 L12: -0.8423
REMARK 3 L13: 0.2584 L23: -0.2483
REMARK 3 S TENSOR
REMARK 3 S11: -0.0437 S12: 0.0792 S13: -0.5563
REMARK 3 S21: 1.2799 S22: -0.2042 S23: 0.5954
REMARK 3 S31: 1.4612 S32: -0.4020 S33: 0.4042
REMARK 3 TLS GROUP : 5
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 300 THROUGH 467 )
REMARK 3 ORIGIN FOR THE GROUP (A): 9.7784 26.1104 5.7806
REMARK 3 T TENSOR
REMARK 3 T11: 0.1341 T22: 0.1142
REMARK 3 T33: 0.0889 T12: 0.0029
REMARK 3 T13: 0.0077 T23: -0.0077
REMARK 3 L TENSOR
REMARK 3 L11: 2.5456 L22: 2.7176
REMARK 3 L33: 1.9943 L12: 0.6066
REMARK 3 L13: -0.5892 L23: 0.2458
REMARK 3 S TENSOR
REMARK 3 S11: -0.0653 S12: 0.2085 S13: -0.1149
REMARK 3 S21: -0.3032 S22: 0.0560 S23: -0.0567
REMARK 3 S31: 0.0868 S32: 0.0073 S33: 0.0070
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 6DSU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-JUN-18.
REMARK 100 THE DEPOSITION ID IS D_1000234749.
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 : 60008
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.980
REMARK 200 RESOLUTION RANGE LOW (A) : 47.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3
REMARK 200 DATA REDUNDANCY : 7.000
REMARK 200 R MERGE (I) : 0.05670
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.7800
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.98
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05
REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : 0.24100
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 (%): 58.39
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.96
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 2.5% MPD, 52% AMMONIUM SULFATE, 0.1M
REMARK 280 MES (PH 5.8), 0.01M MAGNESIUM CHLORIDE, VAPOR DIFFUSION, HANGING
REMARK 280 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 43.72000
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.47950
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 46.69300
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.47950
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 43.72000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 46.69300
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: 4690 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 27980 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -67.0 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 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 NE2 GLN A 656 O2B DZ4 A 905 2.01
REMARK 500 O GLY A 715 NE ARG A 789 2.06
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 GLU A 349 48.98 -77.79
REMARK 500 THR A 350 -58.87 -153.74
REMARK 500 ASP A 402 95.86 -170.78
REMARK 500 ALA A 421 40.21 -87.35
REMARK 500 LEU A 477 -68.09 -120.80
REMARK 500 GLN A 524 157.75 176.75
REMARK 500 GLU A 540 -56.38 -145.57
REMARK 500 THR A 550 -173.46 -60.10
REMARK 500 LEU A 610 -55.26 -124.03
REMARK 500 ASN A 625 26.15 -145.88
REMARK 500 ILE A 628 -33.06 -134.22
REMARK 500 ILE A 716 105.07 58.26
REMARK 500 ASP A 718 -52.19 166.69
REMARK 500 HIS A 768 17.18 82.20
REMARK 500 HIS A 829 -112.23 69.81
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 A1325 DISTANCE = 5.95 ANGSTROMS
REMARK 525 HOH A1326 DISTANCE = 6.04 ANGSTROMS
REMARK 525 HOH A1327 DISTANCE = 6.95 ANGSTROMS
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
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 903
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 904
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue DZ4 A 905
DBREF 6DSU P 1 10 PDB 6DSU 6DSU 1 10
DBREF 6DSU T 4 14 PDB 6DSU 6DSU 4 14
DBREF 6DSU A 297 876 UNP E1C9K5 E1C9K5_GEOSE 1 580
SEQADV 6DSU THR A 550 UNP E1C9K5 SER 254 CONFLICT
SEQRES 1 P 10 DG DC DG DA DT DC DA DC DG DT
SEQRES 1 T 11 DA DC DG DT DG DA DT DC 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 MG A 901 1
HET SO4 A 902 5
HET SO4 A 903 5
HET SO4 A 904 5
HET DZ4 A 905 43
HETNAM MG MAGNESIUM ION
HETNAM SO4 SULFATE ION
HETNAM DZ4 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)
HETNAM 2 DZ4 PHOSPHORYL]AMINO}PHOSPHORYL]ADENOSINE
FORMUL 4 MG MG 2+
FORMUL 5 SO4 3(O4 S 2-)
FORMUL 8 DZ4 C10 H17 N6 O11 P3
FORMUL 9 HOH *343(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 LYS A 383 1 12
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 ILE A 588 VAL A 595 1 8
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 VAL A 713 1 16
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 ALA A 304 0
SHEET 2 AA1 6 GLY A 342 LEU A 346 1 O PHE A 345 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 ILE A 833 N LEU A 826
SHEET 3 AA4 4 TRP A 647 SER A 655 -1 N PHE A 650 O LEU A 834
SHEET 4 AA4 4 LYS A 863 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
LINK MG MG A 901 O3' DZ4 A 905 1555 1555 2.88
CISPEP 1 GLU A 620 PRO A 621 0 -1.86
SITE 1 AC1 4 SER A 655 GLN A 656 DZ4 A 905 HOH A1122
SITE 1 AC2 5 GLU A 667 ASP A 668 ASP A 669 GLY A 745
SITE 2 AC2 5 HOH A1004
SITE 1 AC3 4 ARG A 343 ARG A 677 LYS A 684 MET A 687
SITE 1 AC4 3 SER A 645 SER A 728 ARG A 729
SITE 1 AC5 15 ARG A 615 ASP A 653 TYR A 654 GLN A 656
SITE 2 AC5 15 GLU A 658 HIS A 682 ARG A 702 LYS A 706
SITE 3 AC5 15 VAL A 713 TYR A 714 GLN A 797 ASP A 830
SITE 4 AC5 15 MG A 901 HOH A1122 DT P 10
CRYST1 87.440 93.386 104.959 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 0.011436 0.000000 0.000000 0.00000
SCALE2 0.000000 0.010708 0.000000 0.00000
SCALE3 0.000000 0.000000 0.009528 0.00000