HEADER TRANSFERASE/RNA 22-APR-09 3H5X
TITLE CRYSTAL STRUCTURE OF 2'-AMINO-2'-DEOXY-CYTIDINE-5'-TRIPHOSPHATE BOUND
TITLE 2 TO NOROVIRUS GII RNA POLYMERASE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: RNA DEPENDENT RNA POLYMERASE;
COMPND 3 CHAIN: A;
COMPND 4 EC: 2.7.7.48;
COMPND 5 ENGINEERED: YES;
COMPND 6 MOL_ID: 2;
COMPND 7 MOLECULE: 5'-R(*UP*GP*CP*CP*CP*GP*GP*G)-3';
COMPND 8 CHAIN: P;
COMPND 9 ENGINEERED: YES;
COMPND 10 OTHER_DETAILS: PRIMER RNA;
COMPND 11 MOL_ID: 3;
COMPND 12 MOLECULE: 5'-R(P*UP*GP*CP*CP*CP*GP*GP*GP*C)-3';
COMPND 13 CHAIN: T;
COMPND 14 ENGINEERED: YES;
COMPND 15 OTHER_DETAILS: TEMPLATE RNA
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: NORWALK VIRUS;
SOURCE 3 ORGANISM_TAXID: 11983;
SOURCE 4 STRAIN: AST6139/01/SP;
SOURCE 5 GENE: POLYMERASE;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: XL1-BLUE;
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX-2T;
SOURCE 11 MOL_ID: 2;
SOURCE 12 SYNTHETIC: YES;
SOURCE 13 MOL_ID: 3;
SOURCE 14 SYNTHETIC: YES
KEYWDS POLYMERASE-RNA COMPLEX, NON-NATURAL NUCLEOSIDE TRIPHOSPHATE ANALOG,
KEYWDS 2 CALICIVIRUS, HYDROLASE, NUCLEOTIDE-BINDING, NUCLEOTIDYLTRANSFERASE,
KEYWDS 3 PROTEASE, RNA REPLICATION, RNA-DIRECTED RNA POLYMERASE, THIOL
KEYWDS 4 PROTEASE, TRANSFERASE, TRANSFERASE-RNA COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR D.F.ZAMYATKIN,F.PARRA,A.MACHIN,P.GROCHULSKI,K.K.S.NG
REVDAT 5 06-SEP-23 3H5X 1 REMARK
REVDAT 4 13-OCT-21 3H5X 1 REMARK SEQADV LINK
REVDAT 3 13-JUL-11 3H5X 1 VERSN
REVDAT 2 30-JUN-09 3H5X 1 JRNL
REVDAT 1 19-MAY-09 3H5X 0
JRNL AUTH D.F.ZAMYATKIN,F.PARRA,A.MACHIN,P.GROCHULSKI,K.K.NG
JRNL TITL BINDING OF 2'-AMINO-2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE TO
JRNL TITL 2 NOROVIRUS POLYMERASE INDUCES REARRANGEMENT OF THE ACTIVE
JRNL TITL 3 SITE.
JRNL REF J.MOL.BIOL. V. 390 10 2009
JRNL REFN ISSN 0022-2836
JRNL PMID 19426741
JRNL DOI 10.1016/J.JMB.2009.04.069
REMARK 2
REMARK 2 RESOLUTION. 1.77 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.5.0066
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.77
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.84
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 3 NUMBER OF REFLECTIONS : 62586
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING + TEST SET) : 0.207
REMARK 3 R VALUE (WORKING SET) : 0.205
REMARK 3 FREE R VALUE : 0.246
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 3294
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 20
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.77
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.82
REMARK 3 REFLECTION IN BIN (WORKING SET) : 3984
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0
REMARK 3 BIN R VALUE (WORKING SET) : 0.3340
REMARK 3 BIN FREE R VALUE SET COUNT : 209
REMARK 3 BIN FREE R VALUE : 0.3330
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 3690
REMARK 3 NUCLEIC ACID ATOMS : 344
REMARK 3 HETEROGEN ATOMS : 57
REMARK 3 SOLVENT ATOMS : 441
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 37.10
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.77
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 2.16000
REMARK 3 B22 (A**2) : -1.94000
REMARK 3 B33 (A**2) : -0.22000
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 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.118
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.119
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.086
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.751
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.937
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4227 ; 0.008 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5792 ; 1.074 ; 2.088
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 467 ; 4.929 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 157 ;33.776 ;23.758
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 652 ;12.452 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 23 ;21.280 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 644 ; 0.070 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3025 ; 0.006 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2352 ; 1.556 ; 2.000
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3806 ; 2.499 ; 2.500
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1875 ; 3.408 ; 3.500
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1986 ; 4.782 ; 4.500
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 NCS RESTRAINTS STATISTICS
REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : BABINET MODEL WITH MASK
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.40
REMARK 3 ION PROBE RADIUS : 0.80
REMARK 3 SHRINKAGE RADIUS : 0.80
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 3H5X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-APR-09.
REMARK 100 THE DEPOSITION ID IS D_1000052732.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 22-FEB-08
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 7.0
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : CLSI
REMARK 200 BEAMLINE : 08ID-1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.97934
REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR
REMARK 200 OPTICS : WHITE BEAM SLITS, CRYO-COOLED
REMARK 200 FIRST AND SAGITTALLY BENT SECOND
REMARK 200 CRYSTAL OF DOUBLE CRYSTAL
REMARK 200 MONOCHROMATOR
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : XDS
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 65879
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.770
REMARK 200 RESOLUTION RANGE LOW (A) : 20.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9
REMARK 200 DATA REDUNDANCY : 5.940
REMARK 200 R MERGE (I) : 0.04700
REMARK 200 R SYM (I) : 0.04700
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 21.0000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.77
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97
REMARK 200 COMPLETENESS FOR SHELL (%) : 96.5
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : 0.67000
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: FOURIER SYNTHESIS
REMARK 200 SOFTWARE USED: PHASER
REMARK 200 STARTING MODEL: 3BSO
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 54.63
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.71
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 160 G/L PEG 8000, 250 G/L GLYCEROL,
REMARK 280 100 MM TRIS-CL, PH 7.0, 50 MM KCL, 4 MM MGCL2, 10 MM MNCL2, 14
REMARK 280 MM MERCAPTOETHANOL, 1 G/L CHAPS, VAPOR DIFFUSION, HANGING DROP,
REMARK 280 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 37.30000
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.30000
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 46.85000
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.30000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 37.30000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 46.85000
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: 5840 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 21550 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -65.0 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 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 1
REMARK 465 SER A 2
REMARK 465 ASP A 3
REMARK 465 SER A 4
REMARK 465 LYS A 5
REMARK 465 ARG A 371
REMARK 465 PRO A 372
REMARK 465 ASP A 373
REMARK 465 LYS A 374
REMARK 465 THR A 375
REMARK 465 GLU A 376
REMARK 465 GLY A 377
REMARK 465 LEU A 466
REMARK 465 LYS A 467
REMARK 465 GLU A 468
REMARK 465 GLY A 469
REMARK 465 GLY A 470
REMARK 465 MET A 471
REMARK 465 ASP A 489
REMARK 465 LEU A 490
REMARK 465 SER A 491
REMARK 465 THR A 492
REMARK 465 TRP A 493
REMARK 465 GLU A 494
REMARK 465 GLY A 495
REMARK 465 ASP A 496
REMARK 465 ARG A 497
REMARK 465 ASN A 498
REMARK 465 LEU A 499
REMARK 465 ALA A 500
REMARK 465 PRO A 501
REMARK 465 SER A 502
REMARK 465 PHE A 503
REMARK 465 VAL A 504
REMARK 465 ASN A 505
REMARK 465 GLU A 506
REMARK 465 ASP A 507
REMARK 465 GLY A 508
REMARK 465 VAL A 509
REMARK 465 GLU A 510
REMARK 465 U P 1
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 O3' CSG A 515 O HOH A 738 1.82
REMARK 500 O1 GOL T 509 O HOH T 721 1.97
REMARK 500 CG ARG A 245 OG SER A 248 1.99
REMARK 500 OP1 C P 5 O3 GOL A 517 2.04
REMARK 500 O1B CSG A 515 O HOH A 738 2.09
REMARK 500 OE1 GLN A 96 O HOH A 831 2.14
REMARK 500 OD2 ASP A 247 N2' CSG A 515 2.14
REMARK 500 OD2 ASP A 247 O HOH A 928 2.16
REMARK 500 NE2 GLN A 60 O HOH A 707 2.19
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 ND2 ASN A 92 NE ARG A 477 3654 1.99
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 ALA A 464 -38.68 -39.99
REMARK 500 PHE A 473 133.34 -170.38
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 MN A 514 MN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 99 OD2
REMARK 620 2 GLU A 205 OE2 105.8
REMARK 620 N 1
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MN A 511 MN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 TYR A 243 O
REMARK 620 2 ASP A 343 OD2 89.5
REMARK 620 3 CSG A 515 O2B 96.8 92.4
REMARK 620 4 CSG A 515 O3G 89.8 178.8 86.8
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MN A 512 MN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 343 OD1
REMARK 620 2 CSG A 515 O1A 76.5
REMARK 620 N 1
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MN A 513 MN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 344 OD1
REMARK 620 2 HOH A 563 O 95.8
REMARK 620 3 HOH A 637 O 83.1 87.3
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 MN A 511
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 512
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 513
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 514
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CSG A 515
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 516
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 517
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 518
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL T 509
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3BSO RELATED DB: PDB
REMARK 900 THE SAME PROTEIN BOUND TO CTP
REMARK 900 RELATED ID: 3BSN RELATED DB: PDB
REMARK 900 THE SAME PROTEIN BOUND TO 5-NITROCYTIDINE-5'-TRIPHOSPHATE
REMARK 900 RELATED ID: 1SH0 RELATED DB: PDB
REMARK 900 THE SAME PROTEIN IN A LIGAND-FREE FORM
REMARK 900 RELATED ID: 3H5Y RELATED DB: PDB
DBREF 3H5X A 1 510 UNP Q70ET3 Q70ET3_9CALI 329 838
DBREF 3H5X P 1 8 PDB 3H5X 3H5X 1 8
DBREF 3H5X T 1 9 PDB 3H5X 3H5X 1 9
SEQADV 3H5X SER A 2 UNP Q70ET3 GLY 330 ENGINEERED MUTATION
SEQRES 1 A 510 GLY SER ASP SER LYS GLY THR TYR CYS GLY ALA PRO ILE
SEQRES 2 A 510 LEU GLY PRO GLY SER ALA PRO LYS LEU SER THR LYS THR
SEQRES 3 A 510 LYS PHE TRP ARG SER SER THR ALA PRO LEU PRO PRO GLY
SEQRES 4 A 510 THR TYR GLU PRO ALA TYR LEU GLY GLY LYS ASP PRO ARG
SEQRES 5 A 510 VAL LYS GLY GLY PRO SER LEU GLN GLN VAL MET ARG ASP
SEQRES 6 A 510 GLN LEU LYS PRO PHE THR GLU PRO ARG GLY LYS PRO PRO
SEQRES 7 A 510 LYS PRO SER VAL LEU GLU ALA ALA LYS LYS THR ILE ILE
SEQRES 8 A 510 ASN VAL LEU GLU GLN THR ILE ASP PRO PRO ASP LYS TRP
SEQRES 9 A 510 SER PHE ALA GLN ALA CYS ALA SER LEU ASP LYS THR THR
SEQRES 10 A 510 SER SER GLY HIS PRO HIS HIS MET ARG LYS ASN ASP CYS
SEQRES 11 A 510 TRP ASN GLY GLU SER PHE THR GLY LYS LEU ALA ASP GLN
SEQRES 12 A 510 ALA SER LYS ALA ASN LEU MET PHE GLU GLU GLY LYS ASN
SEQRES 13 A 510 MET THR PRO VAL TYR THR GLY ALA LEU LYS ASP GLU LEU
SEQRES 14 A 510 VAL LYS THR ASP LYS ILE TYR GLY LYS ILE LYS LYS ARG
SEQRES 15 A 510 LEU LEU TRP GLY SER ASP LEU ALA THR MET ILE ARG CYS
SEQRES 16 A 510 ALA ARG ALA PHE GLY GLY LEU MET ASP GLU LEU LYS THR
SEQRES 17 A 510 HIS CYS VAL THR LEU PRO ILE ARG VAL GLY MET ASN MET
SEQRES 18 A 510 ASN GLU ASP GLY PRO ILE ILE PHE GLU ARG HIS SER ARG
SEQRES 19 A 510 TYR ARG TYR HIS TYR ASP ALA ASP TYR SER ARG TRP ASP
SEQRES 20 A 510 SER THR GLN GLN ARG ALA VAL LEU ALA ALA ALA LEU GLU
SEQRES 21 A 510 ILE MET VAL LYS PHE SER SER GLU PRO HIS LEU ALA GLN
SEQRES 22 A 510 VAL VAL ALA GLU ASP LEU LEU SER PRO SER VAL VAL ASP
SEQRES 23 A 510 VAL GLY ASP PHE THR ILE SER ILE ASN GLU GLY LEU PRO
SEQRES 24 A 510 SER GLY VAL PRO CYS THR SER GLN TRP ASN SER ILE ALA
SEQRES 25 A 510 HIS TRP LEU LEU THR LEU CYS ALA LEU SER GLU VAL THR
SEQRES 26 A 510 ASN LEU SER PRO ASP ILE ILE GLN ALA ASN SER LEU PHE
SEQRES 27 A 510 SER PHE TYR GLY ASP ASP GLU ILE VAL SER THR ASP ILE
SEQRES 28 A 510 LYS LEU ASP PRO GLU LYS LEU THR ALA LYS LEU LYS GLU
SEQRES 29 A 510 TYR GLY LEU LYS PRO THR ARG PRO ASP LYS THR GLU GLY
SEQRES 30 A 510 PRO LEU VAL ILE SER GLU ASP LEU ASN GLY LEU THR PHE
SEQRES 31 A 510 LEU ARG ARG THR VAL THR ARG ASP PRO ALA GLY TRP PHE
SEQRES 32 A 510 GLY LYS LEU GLU GLN SER SER ILE LEU ARG GLN MET TYR
SEQRES 33 A 510 TRP THR ARG GLY PRO ASN HIS GLU ASP PRO SER GLU THR
SEQRES 34 A 510 MET ILE PRO HIS SER GLN ARG PRO ILE GLN LEU MET SER
SEQRES 35 A 510 LEU LEU GLY GLU ALA ALA LEU HIS GLY PRO ALA PHE TYR
SEQRES 36 A 510 SER LYS ILE SER LYS LEU VAL ILE ALA GLU LEU LYS GLU
SEQRES 37 A 510 GLY GLY MET ASP PHE TYR VAL PRO ARG GLN GLU PRO MET
SEQRES 38 A 510 PHE ARG TRP MET ARG PHE SER ASP LEU SER THR TRP GLU
SEQRES 39 A 510 GLY ASP ARG ASN LEU ALA PRO SER PHE VAL ASN GLU ASP
SEQRES 40 A 510 GLY VAL GLU
SEQRES 1 P 8 U G C C C G G G
SEQRES 1 T 9 U G C C C G G G C
HET MN A 511 1
HET MN A 512 1
HET MN A 513 1
HET MN A 514 1
HET CSG A 515 29
HET GOL A 516 6
HET GOL A 517 6
HET GOL A 518 6
HET GOL T 509 6
HETNAM MN MANGANESE (II) ION
HETNAM CSG 2'-AMINO-2'-DEOXYCYTIDINE 5'-(TETRAHYDROGEN
HETNAM 2 CSG TRIPHOSPHATE)
HETNAM GOL GLYCEROL
HETSYN CSG 2'-AMINO-2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 4 MN 4(MN 2+)
FORMUL 8 CSG C9 H17 N4 O13 P3
FORMUL 9 GOL 4(C3 H8 O3)
FORMUL 13 HOH *441(H2 O)
HELIX 1 1 SER A 58 GLU A 72 1 15
HELIX 2 2 LYS A 79 ILE A 98 1 20
HELIX 3 3 SER A 105 LEU A 113 1 9
HELIX 4 4 ARG A 126 TRP A 131 5 6
HELIX 5 5 THR A 137 GLU A 153 1 17
HELIX 6 6 THR A 172 GLY A 177 1 6
HELIX 7 7 ASP A 188 HIS A 209 1 22
HELIX 8 8 ASN A 220 ARG A 234 1 15
HELIX 9 9 TRP A 246 GLN A 250 5 5
HELIX 10 10 GLN A 251 SER A 266 1 16
HELIX 11 11 GLU A 268 SER A 281 1 14
HELIX 12 12 CYS A 304 ASN A 326 1 23
HELIX 13 13 SER A 328 ASN A 335 1 8
HELIX 14 14 ASP A 354 TYR A 365 1 12
HELIX 15 15 GLU A 407 ARG A 413 1 7
HELIX 16 16 ARG A 436 LEU A 449 1 14
HELIX 17 17 GLY A 451 GLU A 465 1 15
HELIX 18 18 ARG A 477 SER A 488 1 12
SHEET 1 A 6 THR A 7 TYR A 8 0
SHEET 2 A 6 ALA A 11 PRO A 16 -1 O ALA A 11 N TYR A 8
SHEET 3 A 6 PHE A 290 ILE A 294 -1 O THR A 291 N GLY A 15
SHEET 4 A 6 SER A 283 ASP A 286 -1 N SER A 283 O ILE A 294
SHEET 5 A 6 VAL A 160 LEU A 165 1 N TYR A 161 O ASP A 286
SHEET 6 A 6 LEU A 183 GLY A 186 -1 O LEU A 184 N ALA A 164
SHEET 1 B 2 THR A 26 ARG A 30 0
SHEET 2 B 2 TRP A 417 HIS A 423 -1 O THR A 418 N TRP A 29
SHEET 1 C 2 GLU A 42 PRO A 43 0
SHEET 2 C 2 LEU A 169 VAL A 170 -1 O VAL A 170 N GLU A 42
SHEET 1 D 4 SER A 336 TYR A 341 0
SHEET 2 D 4 ASP A 344 THR A 349 -1 O SER A 348 N LEU A 337
SHEET 3 D 4 TYR A 237 TYR A 243 -1 N TYR A 239 O VAL A 347
SHEET 4 D 4 PRO A 369 THR A 370 -1 O THR A 370 N ASP A 242
SHEET 1 E 3 THR A 389 PHE A 390 0
SHEET 2 E 3 ARG A 393 ASP A 398 -1 O ARG A 393 N PHE A 390
SHEET 3 E 3 GLY A 401 LEU A 406 -1 O PHE A 403 N THR A 396
LINK OD2 ASP A 99 MN MN A 514 1555 1555 2.14
LINK OE2 GLU A 205 MN MN A 514 1555 1555 2.05
LINK O TYR A 243 MN MN A 511 1555 1555 2.30
LINK OD2 ASP A 343 MN MN A 511 1555 1555 2.17
LINK OD1 ASP A 343 MN MN A 512 1555 1555 2.19
LINK OD1 ASP A 344 MN MN A 513 1555 1555 2.14
LINK MN MN A 511 O2B CSG A 515 1555 1555 2.17
LINK MN MN A 511 O3G CSG A 515 1555 1555 2.17
LINK MN MN A 512 O1A CSG A 515 1555 1555 2.19
LINK MN MN A 513 O HOH A 563 1555 1555 2.22
LINK MN MN A 513 O HOH A 637 1555 1555 2.22
CISPEP 1 HIS A 121 PRO A 122 0 -2.97
SITE 1 AC1 4 TYR A 243 ASP A 343 CSG A 515 HOH A 882
SITE 1 AC2 3 ASP A 343 CSG A 515 G P 8
SITE 1 AC3 4 ALA A 241 ASP A 344 HOH A 563 HOH A 637
SITE 1 AC4 4 ASP A 99 GLU A 205 HIS A 209 ASP A 289
SITE 1 AC5 18 ARG A 182 TYR A 243 SER A 244 ARG A 245
SITE 2 AC5 18 TRP A 246 ASP A 247 SER A 300 ASN A 309
SITE 3 AC5 18 ASP A 343 MN A 511 MN A 512 HOH A 738
SITE 4 AC5 18 HOH A 780 HOH A 816 HOH A 883 HOH A 884
SITE 5 AC5 18 G P 8 G T 2
SITE 1 AC6 6 ARG A 30 LEU A 36 ARG A 52 SER A 427
SITE 2 AC6 6 HOH A 635 HOH A 638
SITE 1 AC7 9 LEU A 169 ARG A 413 GLN A 414 TRP A 417
SITE 2 AC7 9 THR A 418 ARG A 419 HOH A 754 C P 5
SITE 3 AC7 9 G P 6
SITE 1 AC8 4 ALA A 256 GLU A 260 GLN A 273 HOH A 682
SITE 1 AC9 9 THR A 117 LYS A 166 G T 2 C T 3
SITE 2 AC9 9 C T 4 HOH T 517 HOH T 721 HOH T 814
SITE 3 AC9 9 HOH T 896
CRYST1 74.600 93.700 96.600 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 0.013405 0.000000 0.000000 0.00000
SCALE2 0.000000 0.010672 0.000000 0.00000
SCALE3 0.000000 0.000000 0.010352 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
