PDB Short entry for 1DV0 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