Header list of 1wwd.pdb file
Complete list - r 2 2 Bytes
HEADER VIRAL PROTEIN/RNA 05-JAN-05 1WWD
TITLE NMR STRUCTURE DETERMINED FOR MLV NC COMPLEX WITH RNA SEQUENCE AACAGU
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-R(P*AP*AP*CP*AP*GP*U)-3';
COMPND 3 CHAIN: B;
COMPND 4 ENGINEERED: YES;
COMPND 5 MOL_ID: 2;
COMPND 6 MOLECULE: NUCLEOPROTEIN P10;
COMPND 7 CHAIN: A;
COMPND 8 SYNONYM: NUCLEOCAPSID PROTEIN;
COMPND 9 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 MOL_ID: 2;
SOURCE 4 ORGANISM_SCIENTIFIC: MOLONEY MURINE LEUKEMIA VIRUS;
SOURCE 5 ORGANISM_TAXID: 11801;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX-6P-1
KEYWDS HYDROPHOBIC GUANOSINE BINDING POCKET, VIRAL PROTEIN-RNA COMPLEX
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR A.DEY,D.YORK,A.SMALLS-MANTEY,M.F.SUMMERS
REVDAT 3 02-MAR-22 1WWD 1 REMARK LINK
REVDAT 2 24-FEB-09 1WWD 1 VERSN
REVDAT 1 22-MAR-05 1WWD 0
JRNL AUTH A.DEY,D.YORK,A.SMALLS-MANTEY,M.F.SUMMERS
JRNL TITL COMPOSITION AND SEQUENCE-DEPENDENT BINDING OF RNA TO THE
JRNL TITL 2 NUCLEOCAPSID PROTEIN OF MOLONEY MURINE LEUKEMIA VIRUS(,)
JRNL REF BIOCHEMISTRY V. 44 3735 2005
JRNL REFN ISSN 0006-2960
JRNL PMID 15751950
JRNL DOI 10.1021/BI047639Q
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : XWINNMR 3.6, CYANA
REMARK 3 AUTHORS : BRUKER (XWINNMR)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS:
REMARK 3 THE STRUCTURES ARE BASED ON A TOTAL OF FOLLOWING RESTRAINTS FOR:
REMARK 3 RNA: 30 INTRARESIDUE RESTRAINTS, 37 INTERMOLECULAR NOE RESTRAINTS
REMARK 3 AND 12 INTER-MOLECULAR H-BOND RESTRAINTS.
REMARK 3 NC PROTEIN: 22 INTRARESIDUE RESTRAINTS AND 40 H-BOND RESTRAINTS
REMARK 4
REMARK 4 1WWD COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-JAN-05.
REMARK 100 THE DEPOSITION ID IS D_1000024078.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 288
REMARK 210 PH : 7.0
REMARK 210 IONIC STRENGTH : 10MM TRIS-HCL, PH 7.0, 10MM
REMARK 210 NACL, 0.1MM ZNCL2
REMARK 210 PRESSURE : 1 ATM
REMARK 210 SAMPLE CONTENTS : UNLABELLED RNA, 1MM RNA
REMARK 210 CONCENTRATION, IN 10MM NACL,
REMARK 210 10MM TRIS-HCL, PH 7.0, 0.1MM
REMARK 210 ZNCL2, 0.1MM BME; UNLABELLED NC
REMARK 210 PROTEIN, 1MM PROTEIN
REMARK 210 CONCENTRATION, IN 10MM NACL,
REMARK 210 10MM TRIS-HCL, PH 7.0, 0.1MM
REMARK 210 ZNCL2, 0.1MM BME
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY
REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ
REMARK 210 SPECTROMETER MODEL : AVANCE; DMX
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : NMRPIPE CURRENT
REMARK 210 METHOD USED : DISTANCE GEOMETRY
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 40
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20
REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D
REMARK 210 HOMONUCLEAR TECHNIQUES
REMARK 215
REMARK 215 NMR STUDY
REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION
REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT
REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON
REMARK 215 THESE RECORDS ARE MEANINGLESS.
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: DIMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
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
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 1 A B 493 C1' - O4' - C4' ANGL. DEV. = 6.2 DEGREES
REMARK 500 1 C B 495 O4' - C4' - C3' ANGL. DEV. = -8.7 DEGREES
REMARK 500 1 C B 495 C1' - O4' - C4' ANGL. DEV. = 7.1 DEGREES
REMARK 500 1 A B 496 O4' - C4' - C3' ANGL. DEV. = -6.6 DEGREES
REMARK 500 1 A B 496 C1' - O4' - C4' ANGL. DEV. = 7.1 DEGREES
REMARK 500 1 G B 497 O4' - C4' - C3' ANGL. DEV. = -7.2 DEGREES
REMARK 500 1 G B 497 C1' - O4' - C4' ANGL. DEV. = 7.2 DEGREES
REMARK 500 1 G B 497 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES
REMARK 500 1 G B 497 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES
REMARK 500 1 G B 497 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES
REMARK 500 1 U B 498 O4' - C4' - C3' ANGL. DEV. = -12.2 DEGREES
REMARK 500 1 U B 498 C1' - O4' - C4' ANGL. DEV. = 4.8 DEGREES
REMARK 500 2 A B 493 O4' - C4' - C3' ANGL. DEV. = -10.9 DEGREES
REMARK 500 2 A B 493 C1' - O4' - C4' ANGL. DEV. = 6.4 DEGREES
REMARK 500 2 C B 495 O4' - C4' - C3' ANGL. DEV. = -8.0 DEGREES
REMARK 500 2 C B 495 C1' - O4' - C4' ANGL. DEV. = 7.3 DEGREES
REMARK 500 2 A B 496 O4' - C4' - C3' ANGL. DEV. = -7.2 DEGREES
REMARK 500 2 A B 496 C1' - O4' - C4' ANGL. DEV. = 7.3 DEGREES
REMARK 500 2 G B 497 O4' - C4' - C3' ANGL. DEV. = -7.6 DEGREES
REMARK 500 2 G B 497 C1' - O4' - C4' ANGL. DEV. = 6.9 DEGREES
REMARK 500 2 G B 497 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES
REMARK 500 2 G B 497 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES
REMARK 500 2 G B 497 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES
REMARK 500 2 U B 498 O4' - C4' - C3' ANGL. DEV. = -13.1 DEGREES
REMARK 500 3 A B 493 O4' - C4' - C3' ANGL. DEV. = -8.7 DEGREES
REMARK 500 3 A B 493 C1' - O4' - C4' ANGL. DEV. = 7.1 DEGREES
REMARK 500 3 A B 494 O4' - C4' - C3' ANGL. DEV. = -13.0 DEGREES
REMARK 500 3 C B 495 O4' - C4' - C3' ANGL. DEV. = -7.5 DEGREES
REMARK 500 3 C B 495 C1' - O4' - C4' ANGL. DEV. = 7.3 DEGREES
REMARK 500 3 A B 496 O4' - C4' - C3' ANGL. DEV. = -8.0 DEGREES
REMARK 500 3 A B 496 C1' - O4' - C4' ANGL. DEV. = 7.4 DEGREES
REMARK 500 3 G B 497 O4' - C4' - C3' ANGL. DEV. = -7.2 DEGREES
REMARK 500 3 G B 497 C1' - O4' - C4' ANGL. DEV. = 6.9 DEGREES
REMARK 500 3 G B 497 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES
REMARK 500 3 G B 497 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES
REMARK 500 3 G B 497 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES
REMARK 500 3 U B 498 O4' - C4' - C3' ANGL. DEV. = -12.5 DEGREES
REMARK 500 4 A B 493 O4' - C4' - C3' ANGL. DEV. = -7.3 DEGREES
REMARK 500 4 A B 493 C1' - O4' - C4' ANGL. DEV. = 7.2 DEGREES
REMARK 500 4 A B 494 O4' - C4' - C3' ANGL. DEV. = -12.9 DEGREES
REMARK 500 4 C B 495 O4' - C4' - C3' ANGL. DEV. = -7.5 DEGREES
REMARK 500 4 C B 495 C1' - O4' - C4' ANGL. DEV. = 7.4 DEGREES
REMARK 500 4 A B 496 O4' - C4' - C3' ANGL. DEV. = -7.8 DEGREES
REMARK 500 4 A B 496 C1' - O4' - C4' ANGL. DEV. = 7.5 DEGREES
REMARK 500 4 G B 497 O4' - C4' - C3' ANGL. DEV. = -8.3 DEGREES
REMARK 500 4 G B 497 C1' - O4' - C4' ANGL. DEV. = 7.0 DEGREES
REMARK 500 4 G B 497 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES
REMARK 500 4 G B 497 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES
REMARK 500 4 G B 497 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES
REMARK 500 4 U B 498 O4' - C4' - C3' ANGL. DEV. = -12.0 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 238 ANGLE DEVIATIONS.
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 1 GLU A 15 126.37 -177.81
REMARK 500 1 ARG A 17 51.75 -179.93
REMARK 500 1 ARG A 18 54.74 -179.88
REMARK 500 1 SER A 19 -150.43 39.36
REMARK 500 1 GLN A 20 30.90 -91.02
REMARK 500 1 LEU A 21 88.05 -57.06
REMARK 500 1 ALA A 27 34.43 -99.78
REMARK 500 1 TYR A 28 -58.04 -129.38
REMARK 500 1 LYS A 30 25.85 90.16
REMARK 500 1 GLN A 52 106.48 -167.06
REMARK 500 2 GLN A 7 -58.08 -153.36
REMARK 500 2 GLU A 15 74.77 -108.37
REMARK 500 2 ARG A 17 119.53 179.44
REMARK 500 2 ARG A 18 76.94 -118.85
REMARK 500 2 TYR A 28 -57.62 -129.76
REMARK 500 2 LYS A 30 24.08 89.03
REMARK 500 2 GLN A 52 88.25 65.37
REMARK 500 3 VAL A 4 -48.73 -134.73
REMARK 500 3 GLN A 7 -61.09 -157.15
REMARK 500 3 ASP A 10 98.29 59.70
REMARK 500 3 GLN A 12 -67.70 -92.59
REMARK 500 3 ARG A 17 171.77 53.36
REMARK 500 3 ARG A 18 52.62 -148.13
REMARK 500 3 GLN A 20 51.52 38.88
REMARK 500 3 LEU A 21 89.91 -54.13
REMARK 500 3 ALA A 27 34.44 -97.21
REMARK 500 3 TYR A 28 -60.45 -130.28
REMARK 500 3 LYS A 30 23.06 89.20
REMARK 500 3 GLN A 52 76.81 49.30
REMARK 500 3 SER A 54 106.87 60.36
REMARK 500 4 GLN A 7 75.46 -158.01
REMARK 500 4 ARG A 11 -54.98 -179.86
REMARK 500 4 GLN A 12 135.56 64.98
REMARK 500 4 SER A 19 -150.58 39.23
REMARK 500 4 GLN A 20 31.70 -91.08
REMARK 500 4 LEU A 21 82.92 -65.47
REMARK 500 4 ALA A 27 35.88 -98.83
REMARK 500 4 TYR A 28 -53.29 -131.20
REMARK 500 4 LYS A 30 22.27 88.07
REMARK 500 4 SER A 54 147.54 -173.75
REMARK 500 5 GLN A 9 167.57 55.32
REMARK 500 5 ARG A 11 -61.85 -168.20
REMARK 500 5 GLU A 15 144.97 63.02
REMARK 500 5 ARG A 16 -51.79 -128.33
REMARK 500 5 ARG A 18 77.01 -100.38
REMARK 500 5 SER A 19 96.26 -42.75
REMARK 500 5 GLN A 20 50.95 38.49
REMARK 500 5 ALA A 27 33.83 -95.94
REMARK 500 5 TYR A 28 -57.74 -127.99
REMARK 500 5 LYS A 30 21.26 89.60
REMARK 500
REMARK 500 THIS ENTRY HAS 242 RAMACHANDRAN OUTLIERS.
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 ZN A 57 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 26 SG
REMARK 620 2 CYS A 29 SG 109.3
REMARK 620 3 HIS A 34 NE2 108.4 108.3
REMARK 620 4 CYS A 39 SG 106.6 106.7 117.4
REMARK 620 N 1 2 3
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 57
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1WWE RELATED DB: PDB
REMARK 900 NMR STRUCTURE DETERMINED FOR MLV NC COMPLEX WITH RNA SEQUENCE
REMARK 900 UUUUGCU
REMARK 900 RELATED ID: 1WWF RELATED DB: PDB
REMARK 900 NMR STRUCTURE DETERMINED FOR MLV NC COMPLEX WITH RNA SEQUENCE
REMARK 900 CCUCCGU
REMARK 900 RELATED ID: 1WWG RELATED DB: PDB
REMARK 900 NMR STRUCTURE DETERMINED FOR MLV NC COMPLEX WITH RNA SEQUENCE UAUCUG
DBREF 1WWD A 1 56 UNP P03332 GAG_MLVMO 479 534
DBREF 1WWD B 493 498 PDB 1WWD 1WWD 493 498
SEQRES 1 B 6 A A C A G U
SEQRES 1 A 56 ALA THR VAL VAL SER GLY GLN LYS GLN ASP ARG GLN GLY
SEQRES 2 A 56 GLY GLU ARG ARG ARG SER GLN LEU ASP ARG ASP GLN CYS
SEQRES 3 A 56 ALA TYR CYS LYS GLU LYS GLY HIS TRP ALA LYS ASP CYS
SEQRES 4 A 56 PRO LYS LYS PRO ARG GLY PRO ARG GLY PRO ARG PRO GLN
SEQRES 5 A 56 THR SER LEU LEU
HET ZN A 57 1
HETNAM ZN ZINC ION
FORMUL 3 ZN ZN 2+
HELIX 1 1 TRP A 35 CYS A 39 5 5
LINK SG CYS A 26 ZN ZN A 57 1555 1555 2.31
LINK SG CYS A 29 ZN ZN A 57 1555 1555 2.31
LINK NE2 HIS A 34 ZN ZN A 57 1555 1555 1.99
LINK SG CYS A 39 ZN ZN A 57 1555 1555 2.30
CISPEP 1 GLY A 45 PRO A 46 1 -0.06
CISPEP 2 GLY A 45 PRO A 46 2 0.06
CISPEP 3 GLY A 45 PRO A 46 3 -0.04
CISPEP 4 GLY A 45 PRO A 46 4 0.04
CISPEP 5 GLY A 45 PRO A 46 5 -0.09
CISPEP 6 GLY A 45 PRO A 46 6 -0.02
CISPEP 7 GLY A 45 PRO A 46 7 0.01
CISPEP 8 GLY A 45 PRO A 46 8 0.02
CISPEP 9 GLY A 45 PRO A 46 9 0.01
CISPEP 10 GLY A 45 PRO A 46 10 -0.12
CISPEP 11 GLY A 45 PRO A 46 11 -0.09
CISPEP 12 GLY A 45 PRO A 46 12 0.09
CISPEP 13 GLY A 45 PRO A 46 13 -0.01
CISPEP 14 GLY A 45 PRO A 46 14 -0.06
CISPEP 15 GLY A 45 PRO A 46 15 0.02
CISPEP 16 GLY A 45 PRO A 46 16 0.08
CISPEP 17 GLY A 45 PRO A 46 17 -0.06
CISPEP 18 GLY A 45 PRO A 46 18 0.00
CISPEP 19 GLY A 45 PRO A 46 19 -0.04
CISPEP 20 GLY A 45 PRO A 46 20 -0.08
SITE 1 AC1 4 CYS A 26 CYS A 29 HIS A 34 CYS A 39
CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1
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 1.000000 0.000000 0.000000 0.00000
SCALE2 0.000000 1.000000 0.000000 0.00000
SCALE3 0.000000 0.000000 1.000000 0.00000
MODEL 1
Complete list - r 2 2 Bytes