10 20 30 40 50 60 70 80 1DV0 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA BINDING PROTEIN 19-JAN-00 1DV0
TITLE REFINED NMR SOLUTION STRUCTURE OF THE C-TERMINAL UBA DOMAIN TITLE 2 OF THE 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 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 JRNL TITL 2 INTERACTION BETWEEN THE UBA(2) DOMAIN OF THE DNA JRNL TITL 3 REPAIR PROTEIN HHR23A 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, REMARK 1 AUTH 2 C.F.LIU,I.S.CHEN,J.FEIGON REMARK 1 TITL STRUCTURE OF A HUMAN DNA REPAIR PROTEIN UBA DOMAIN REMARK 1 TITL 2 THAT 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 : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL REMARK 3 OF 796 RESTRAINTS, 779 ARE NOE-DERIVED, 17 DISTANCE RESTRAINTS REMARK 3 ARE 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 RCSB ID CODE IS RCSB010394.
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 REMARK 210 PHOSPHATE, 100MM SODIUM REMARK 210 CHLORIDE, 95% H2O, 5% D2O; 2MM REMARK 210 UBA-DOMAIN, U-15N, 50MM SODIUM REMARK 210 PHOSPHATE, 100MM SODIUM REMARK 210 CHLORIDE, 95% H2O, 5% D2O; 2MM REMARK 210 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-SEPARATED_ REMARK 210 NOESY, 3D_15N-SEPARATED_NOESY, REMARK 210 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 : XWINNMR 1.3, XEASY 1.3.10, X- REMARK 210 PLOR 3.1 REMARK 210 METHOD USED : SIMULATED ANNEALING, REMARK 210 MOLECULAR 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 REMARK 210 VIOLATIONS, STRUCTURES WITH REMARK 210 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 REMARK 210 NMR 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 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 10 LYS A 28 45.63 27.14 REMARK 500 10 GLU A 30 -70.30 85.66 REMARK 500 10 SER A 39 17.10 -140.74 REMARK 500 10 GLN A 40 127.02 -39.21 REMARK 500 10 PHE A 42 -161.07 -103.33 REMARK 500 10 ASP A 43 99.27 -165.57 REMARK 500 11 GLU A 27 75.10 62.23 REMARK 500 11 LYS A 28 51.81 23.78 REMARK 500 11 SER A 39 30.03 -145.61 REMARK 500 11 ASN A 41 -154.00 -112.45 REMARK 500 11 PHE A 42 -79.27 -118.35 REMARK 500 11 ASP A 43 14.98 -160.11 REMARK 500 11 ASP A 44 106.90 63.69 REMARK 500 12 GLU A 27 72.80 62.91 REMARK 500 12 LYS A 28 39.08 31.58 REMARK 500 12 GLN A 40 -91.88 40.18 REMARK 500 12 ASN A 41 -46.12 -161.21 REMARK 500 12 ASP A 43 165.98 167.53 REMARK 500 13 LYS A 3 -32.60 -32.99 REMARK 500 13 LYS A 28 46.31 27.65 REMARK 500 13 GLU A 30 -67.77 85.59 REMARK 500 13 GLN A 40 27.56 45.91 REMARK 500 13 ASP A 43 -94.72 66.42 REMARK 500 14 GLU A 2 20.28 -167.07 REMARK 500 14 GLU A 27 70.49 67.37 REMARK 500 14 LYS A 28 32.68 36.85 REMARK 500 14 ASN A 41 -83.53 -46.44 REMARK 500 14 ASP A 44 -57.72 -162.85 REMARK 500 15 GLU A 27 73.38 58.70 REMARK 500 15 LYS A 28 42.43 30.68 REMARK 500 15 PHE A 42 -55.51 -165.50 REMARK 500 16 LYS A 3 -28.51 -38.16 REMARK 500 16 GLU A 27 72.28 63.87 REMARK 500 16 LYS A 28 38.38 32.46 REMARK 500 16 ASP A 43 70.84 169.64 REMARK 500 17 LYS A 3 -29.15 -35.25 REMARK 500 17 GLU A 27 77.91 61.41 REMARK 500 17 LYS A 28 47.11 27.83 REMARK 500 17 GLN A 40 100.53 -42.85 REMARK 500 17 ASN A 41 -169.17 -128.69 REMARK 500 17 PHE A 42 49.42 -151.57 REMARK 500 17 ASP A 43 74.83 -151.39 REMARK 500 18 GLU A 27 66.49 61.57 REMARK 500 18 LYS A 28 42.46 31.12 REMARK 500 18 GLU A 30 -73.24 84.64 REMARK 500 18 SER A 39 15.95 -142.93 REMARK 500 18 GLN A 40 88.81 -33.04 REMARK 500 18 PHE A 42 157.22 67.31 REMARK 500 18 ASP A 43 -60.27 -120.08 REMARK 500 18 ASP A 44 -69.91 -140.42 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