PDB Short entry for 1PVE HEADER DNA BINDING PROTEIN 27-JUN-03 1PVE TITLE SOLUTION STRUCTURE OF XPC BINDING DOMAIN OF HHR23B COMPND MOL_ID: 1; COMPND 2 MOLECULE: UV EXCISION REPAIR PROTEIN RAD23 HOMOLOG B; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: XPC BINDING DOMAIN; COMPND 5 SYNONYM: HHR23B; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: HH23B; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS HHR23B, XPC BINDING DOMAIN, NMR SOLUTION STRUCTURE, NUCLEOTIDE KEYWDS 2 EXCISION REPAIR, CHAPS, DNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR B.KIM,K.-S.RYU,H.J.KIM,B.-S.CHOI REVDAT 4 02-MAR-22 1PVE 1 REMARK SEQADV REVDAT 3 24-FEB-09 1PVE 1 VERSN REVDAT 2 21-JUN-05 1PVE 1 JRNL REVDAT 1 10-AUG-04 1PVE 0 JRNL AUTH B.KIM,K.S.RYU,H.J.KIM,S.J.CHO,B.S.CHOI JRNL TITL SOLUTION STRUCTURE AND BACKBONE DYNAMICS OF THE XPC-BINDING JRNL TITL 2 DOMAIN OF THE HUMAN DNA REPAIR PROTEIN HHR23B. JRNL REF FEBS J. V. 272 2467 2005 JRNL REFN ISSN 1742-464X JRNL PMID 15885096 JRNL DOI 10.1111/J.1742-4658.2005.04667.X REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 6.3C, AMBER 7 REMARK 3 AUTHORS : VARIAN (VNMR), DAVID A. CASE ETC (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1PVE COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-JUL-03. REMARK 100 THE DEPOSITION ID IS D_1000019601. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 40MM SODIUM PHOSPHATE, 160MM REMARK 210 SODIUM CHLORIDE, 10MM CHAPS REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1MM HHR23B(275-342) U-15N, 13C; REMARK 210 40MM PHOSPHATE BUFFER NA; 10MM REMARK 210 CHAPS NA REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY; HNHA REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, CYANA 1.6 REMARK 210 METHOD USED : AUTOMATIC NOE ASSIGNMENT, REMARK 210 DISTANCE GEOMETRY, SIMULATED REMARK 210 ANNEALING, MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 20 REMARK 210 REMARK 210 REMARK: THE STRUCTURES ARE BASED ON A TOTAL OF 1312 RESTRAINTS, REMARK 210 1242 ARE NOE-DERIVED DISTANCE CONSTRAINTS, 70 DIHEDRAL ANGLE REMARK 210 RESTRAINTS ( 14 FROM JHNHA AND 56 FROM TALOS) 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 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 3 ARG A 10 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 3 ARG A 19 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 6 ARG A 19 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 7 ARG A 10 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 7 ARG A 19 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 11 ARG A 19 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 12 ARG A 10 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 12 ARG A 19 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 13 ARG A 10 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 13 ARG A 19 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 14 ARG A 19 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 15 ARG A 19 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 16 ARG A 19 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 18 ARG A 19 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 20 ARG A 19 NE - CZ - NH1 ANGL. DEV. = 3.3 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 MET A 4 86.22 -156.16 REMARK 500 1 GLN A 17 -47.68 -130.75 REMARK 500 3 SER A 2 37.78 -153.96 REMARK 500 3 LEU A 6 -10.02 61.53 REMARK 500 3 HIS A 50 28.47 -141.63 REMARK 500 3 ALA A 65 -10.39 -144.76 REMARK 500 4 GLN A 17 -50.46 -128.83 REMARK 500 4 ASN A 40 73.35 -154.16 REMARK 500 4 HIS A 50 20.80 -140.63 REMARK 500 5 HIS A 50 24.30 -141.69 REMARK 500 5 GLU A 64 -166.03 58.96 REMARK 500 6 LEU A 6 20.00 57.64 REMARK 500 6 ARG A 10 26.97 -69.97 REMARK 500 6 PRO A 61 154.25 -49.91 REMARK 500 7 GLN A 23 2.75 -67.87 REMARK 500 7 ASN A 40 73.20 -151.87 REMARK 500 8 GLU A 7 -26.52 -150.57 REMARK 500 8 GLN A 23 2.30 -68.91 REMARK 500 9 LEU A 6 -6.57 60.94 REMARK 500 10 ASN A 11 19.79 -144.46 REMARK 500 10 GLN A 17 -51.15 -128.12 REMARK 500 10 GLN A 23 2.26 -67.95 REMARK 500 10 ASN A 40 72.90 -151.84 REMARK 500 10 GLN A 63 -2.65 63.32 REMARK 500 11 MET A 4 153.19 65.43 REMARK 500 11 GLN A 23 0.68 -66.40 REMARK 500 11 ASN A 40 72.69 -153.66 REMARK 500 12 ASN A 11 22.22 -144.23 REMARK 500 12 GLN A 14 -22.96 48.56 REMARK 500 12 GLN A 17 -51.26 -131.68 REMARK 500 12 GLU A 64 -42.96 72.41 REMARK 500 12 ALA A 65 -8.47 -141.61 REMARK 500 13 GLN A 14 -15.98 59.14 REMARK 500 13 GLN A 23 1.44 -69.13 REMARK 500 13 ASN A 40 76.13 -158.82 REMARK 500 13 HIS A 50 27.52 -141.18 REMARK 500 13 GLU A 64 -40.51 -137.92 REMARK 500 13 ALA A 65 18.90 47.78 REMARK 500 14 ALA A 65 -28.49 58.19 REMARK 500 15 MET A 4 21.77 -151.06 REMARK 500 15 ARG A 10 2.52 -69.72 REMARK 500 16 ASN A 40 74.75 -155.19 REMARK 500 17 SER A 2 91.54 -69.68 REMARK 500 17 GLN A 17 -42.04 -135.02 REMARK 500 17 HIS A 50 26.18 -140.78 REMARK 500 18 SER A 2 -31.17 -142.20 REMARK 500 18 HIS A 3 -22.21 -150.70 REMARK 500 18 ASN A 40 61.26 -151.36 REMARK 500 18 GLN A 63 17.69 55.48 REMARK 500 18 GLU A 64 -31.46 -147.11 REMARK 500 REMARK 500 THIS ENTRY HAS 61 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 20 ARG A 19 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1PVE A 5 72 UNP P54727 RD23B_HUMAN 275 342 SEQADV 1PVE GLY A 1 UNP P54727 CLONING ARTIFACT SEQADV 1PVE SER A 2 UNP P54727 CLONING ARTIFACT SEQADV 1PVE HIS A 3 UNP P54727 CLONING ARTIFACT SEQADV 1PVE MET A 4 UNP P54727 CLONING ARTIFACT SEQRES 1 A 72 GLY SER HIS MET PRO LEU GLU PHE LEU ARG ASN GLN PRO SEQRES 2 A 72 GLN PHE GLN GLN MET ARG GLN ILE ILE GLN GLN ASN PRO SEQRES 3 A 72 SER LEU LEU PRO ALA LEU LEU GLN GLN ILE GLY ARG GLU SEQRES 4 A 72 ASN PRO GLN LEU LEU GLN GLN ILE SER GLN HIS GLN GLU SEQRES 5 A 72 HIS PHE ILE GLN MET LEU ASN GLU PRO VAL GLN GLU ALA SEQRES 6 A 72 GLY GLY GLN GLY GLY GLY GLY HELIX 1 1 LEU A 6 ARG A 10 5 5 HELIX 2 2 GLN A 17 GLN A 23 1 7 HELIX 3 3 ASN A 25 SER A 27 5 3 HELIX 4 4 LEU A 28 ARG A 38 1 11 HELIX 5 5 ASN A 40 GLN A 49 1 10 HELIX 6 6 HIS A 50 GLU A 60 1 11 HELIX 7 7 GLU A 64 GLY A 69 5 6 CISPEP 1 GLY A 71 GLY A 72 8 -0.26 CISPEP 2 GLY A 67 GLN A 68 9 -3.55 CISPEP 3 SER A 2 HIS A 3 16 -0.77 CISPEP 4 GLU A 64 ALA A 65 19 -7.18 CISPEP 5 GLY A 67 GLN A 68 19 -4.85 CISPEP 6 GLY A 71 GLY A 72 19 -5.20 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