Header list of 1dv0.pdb file
Complete list - b 16 2 Bytes
HEADER DNA BINDING PROTEIN 19-JAN-00 1DV0
TITLE REFINED NMR SOLUTION STRUCTURE OF THE C-TERMINAL UBA DOMAIN OF THE
TITLE 2 HUMAN HOMOLOGUE OF RAD23A (HHR23A)
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA REPAIR PROTEIN HHR23A;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: UBA DOMAIN (C-TERMINAL DOMAIN);
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PGEX-2T (PHARMACIA)
KEYWDS HELICAL BUNDLE, DNA BINDING PROTEIN
EXPDTA SOLUTION NMR
NUMMDL 18
AUTHOR E.S.WITHERS-WARD,T.D.MUELLER,I.S.CHEN,J.FEIGON
REVDAT 4 16-FEB-22 1DV0 1 REMARK
REVDAT 3 24-FEB-09 1DV0 1 VERSN
REVDAT 2 29-MAR-05 1DV0 1 JRNL REMARK
REVDAT 1 11-FEB-00 1DV0 0
SPRSDE 11-FEB-00 1DV0 1UBA
JRNL AUTH E.S.WITHERS-WARD,T.D.MUELLER,I.S.CHEN,J.FEIGON
JRNL TITL BIOCHEMICAL AND STRUCTURAL ANALYSIS OF THE INTERACTION
JRNL TITL 2 BETWEEN THE UBA(2) DOMAIN OF THE DNA REPAIR PROTEIN HHR23A
JRNL TITL 3 AND HIV-1 VPR
JRNL REF BIOCHEMISTRY V. 39 14103 2000
JRNL REFN ISSN 0006-2960
JRNL PMID 11087358
JRNL DOI 10.1021/BI0017071
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH T.DIECKMANN,E.S.WITHERS-WARD,M.A.JAROSINSKI,C.F.LIU,
REMARK 1 AUTH 2 I.S.CHEN,J.FEIGON
REMARK 1 TITL STRUCTURE OF A HUMAN DNA REPAIR PROTEIN UBA DOMAIN THAT
REMARK 1 TITL 2 INTERACTS WITH HIV-1 VPR
REMARK 1 REF NAT.STRUCT.BIOL. V. 5 1042 1998
REMARK 1 REFN ISSN 1072-8368
REMARK 1 DOI 10.1038/4220
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : XWINNMR 1.3, X-PLOR 3.1
REMARK 3 AUTHORS : BRUKER (XWINNMR), BRUNGER (X-PLOR)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL OF
REMARK 3 796 RESTRAINTS, 779 ARE NOE-DERIVED, 17 DISTANCE RESTRAINTS ARE
REMARK 3 FROM HYDROGEN BONDS
REMARK 4
REMARK 4 1DV0 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-JAN-00.
REMARK 100 THE DEPOSITION ID IS D_1000010394.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 300
REMARK 210 PH : 6.5
REMARK 210 IONIC STRENGTH : 50MM SODIUM PHOSPHATE, 100MM
REMARK 210 SODIUM CHLORIDE
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 1MM UBA-DOMAIN, CHEMICALLY
REMARK 210 SYNTHESIZED; 50MM POTASSIUM
REMARK 210 PHOSPHATE PH 6.5; 90% H2O, 10%
REMARK 210 D2O; 2MM UBA-DOMAIN, EXPRESSED
REMARK 210 IN E.COLI, 50MM SODIUM PHOSPHATE,
REMARK 210 100MM SODIUM CHLORIDE, 95% H2O,
REMARK 210 5% D2O; 2MM UBA-DOMAIN, U-15N,
REMARK 210 50MM SODIUM PHOSPHATE, 100MM
REMARK 210 SODIUM CHLORIDE, 95% H2O, 5% D2O;
REMARK 210 2MM UBA-DOMAIN, U-15N,13C, 50MM
REMARK 210 SODIUM PHOSPHATE, 100MM SODIUM
REMARK 210 CHLORIDE, 95% H2O, 5% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 3D_13C
REMARK 210 -SEPARATED_NOESY; 3D_15N-
REMARK 210 SEPARATED_NOESY; DQF-COSY
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ
REMARK 210 SPECTROMETER MODEL : DRX
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : XEASY 1.3.10, X-PLOR 3.1
REMARK 210 METHOD USED : SIMULATED ANNEALING, MOLECULAR
REMARK 210 DYNAMICS
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 100
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 18
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH FAVORABLE NON
REMARK 210 -BOND ENERGY, STRUCTURES WITH
REMARK 210 THE LEAST RESTRAINT VIOLATIONS,
REMARK 210 STRUCTURES WITH THE LOWEST ENERGY
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 6
REMARK 210
REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR
REMARK 210 SPECTROSCOPY
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: MONOMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465 MODELS 1-18
REMARK 465 RES C SSSEQI
REMARK 465 GLY A -1
REMARK 465 SER A 0
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 2 GLU A 45 C GLU A 45 OXT -0.140
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 2 GLU A 45 CA - C - O ANGL. DEV. = -12.8 DEGREES
REMARK 500 13 TYR A 23 CB - CG - CD1 ANGL. DEV. = -3.7 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 1 GLU A 27 69.04 61.63
REMARK 500 1 LYS A 28 45.66 26.45
REMARK 500 1 PHE A 42 91.07 -52.99
REMARK 500 1 ASP A 43 134.29 175.79
REMARK 500 2 GLU A 2 -4.62 85.52
REMARK 500 2 GLU A 27 74.32 62.37
REMARK 500 2 LYS A 28 42.00 27.21
REMARK 500 2 GLN A 40 61.85 -108.16
REMARK 500 2 ASN A 41 -157.49 -149.42
REMARK 500 3 GLU A 2 -23.04 86.74
REMARK 500 3 GLU A 27 67.12 64.52
REMARK 500 3 LYS A 28 41.99 30.92
REMARK 500 3 ASN A 41 -89.12 -120.59
REMARK 500 3 PHE A 42 31.58 -178.45
REMARK 500 3 ASP A 43 -178.17 69.06
REMARK 500 4 GLU A 27 70.72 64.69
REMARK 500 4 LYS A 28 36.81 33.32
REMARK 500 4 ASN A 41 -75.19 -116.96
REMARK 500 4 PHE A 42 -161.05 -171.23
REMARK 500 4 ASP A 44 90.82 -170.78
REMARK 500 5 GLU A 27 73.82 59.26
REMARK 500 5 LYS A 28 50.44 27.12
REMARK 500 5 SER A 39 23.59 -149.33
REMARK 500 5 ASN A 41 -69.10 -161.51
REMARK 500 5 ASP A 43 109.17 169.04
REMARK 500 5 ASP A 44 91.66 59.25
REMARK 500 6 GLU A 27 74.79 61.02
REMARK 500 6 LYS A 28 42.73 29.82
REMARK 500 6 GLN A 40 90.65 -38.35
REMARK 500 6 PHE A 42 52.84 79.24
REMARK 500 7 GLU A 27 74.53 62.27
REMARK 500 7 LYS A 28 41.59 25.85
REMARK 500 7 GLN A 40 125.78 -34.71
REMARK 500 7 ASN A 41 170.57 -56.79
REMARK 500 7 PHE A 42 -60.59 -159.02
REMARK 500 7 ASP A 43 96.85 179.12
REMARK 500 8 TYR A 23 -61.98 -90.55
REMARK 500 8 GLU A 27 69.36 60.93
REMARK 500 8 LYS A 28 43.06 26.44
REMARK 500 8 GLN A 40 37.84 -91.62
REMARK 500 8 PHE A 42 -93.18 -87.84
REMARK 500 8 ASP A 44 60.83 -153.70
REMARK 500 9 LYS A 3 -31.62 -37.48
REMARK 500 9 GLU A 27 72.01 60.94
REMARK 500 9 LYS A 28 41.44 32.79
REMARK 500 9 GLN A 40 78.54 -116.29
REMARK 500 9 ASN A 41 -150.34 -156.10
REMARK 500 9 PHE A 42 -66.99 -155.17
REMARK 500 10 GLU A 2 -30.00 -173.55
REMARK 500 10 LYS A 3 -32.53 -36.66
REMARK 500
REMARK 500 THIS ENTRY HAS 100 RAMACHANDRAN OUTLIERS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1UBA RELATED DB: PDB
REMARK 900 LOW RESOLUTION STRUCTURE OF THE UBA DOMAIN OF HHR23A
DBREF 1DV0 A 1 45 UNP P54725 RD23A_HUMAN 319 363
SEQADV 1DV0 GLY A -1 UNP P54725 SEE REMARK 999
SEQADV 1DV0 SER A 0 UNP P54725 SEE REMARK 999
SEQRES 1 A 47 GLY SER GLN GLU LYS GLU ALA ILE GLU ARG LEU LYS ALA
SEQRES 2 A 47 LEU GLY PHE PRO GLU SER LEU VAL ILE GLN ALA TYR PHE
SEQRES 3 A 47 ALA CYS GLU LYS ASN GLU ASN LEU ALA ALA ASN PHE LEU
SEQRES 4 A 47 LEU SER GLN ASN PHE ASP ASP GLU
HELIX 1 1 GLU A 2 GLU A 7 1 6
HELIX 2 2 PRO A 15 PHE A 24 1 10
HELIX 3 3 ASN A 29 LEU A 37 1 9
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 - b 16 2 Bytes