HEADER TRANSFERASE 25-AUG-06 2I5O TITLE SOLUTION STRUCTURE OF THE UBIQUITIN-BINDING ZINC FINGER (UBZ) DOMAIN TITLE 2 OF THE HUMAN DNA Y-POLYMERASE ETA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE ETA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UBIQUITIN-BINDING ZINC FINGER (UBZ); COMPND 5 SYNONYM: RAD30 HOMOLOG A, XERODERMA PIGMENTOSUM VARIANT TYPE PROTEIN; COMPND 6 EC: 2.7.7.7; COMPND 7 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: POLH; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)STAR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS ZINC FINGER, DNA POLYMERASE, POL ETA, UBZ, UBIQUITIN-BINDING ZINC KEYWDS 2 FINGER, TRANSLESION SYNTHESIS, UBIQUITIN-BINDING DOMAIN, TRANSFERASE EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR P.ZHOU,M.G.BOMAR REVDAT 3 09-MAR-22 2I5O 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 2I5O 1 VERSN REVDAT 1 13-MAR-07 2I5O 0 JRNL AUTH M.G.BOMAR,M.T.PAI,S.R.TZENG,S.S.LI,P.ZHOU JRNL TITL STRUCTURE OF THE UBIQUITIN-BINDING ZINC FINGER DOMAIN OF JRNL TITL 2 HUMAN DNA Y-POLYMERASE ETA. JRNL REF EMBO REP. V. 8 247 2007 JRNL REFN ISSN 1469-221X JRNL PMID 17304240 JRNL DOI 10.1038/SJ.EMBOR.7400901 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 2.1, XPLOR-NIH 2.9.7 REMARK 3 AUTHORS : GUENTERT (CYANA), SCHWIETERS (XPLOR-NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2I5O COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-AUG-06. REMARK 100 THE DEPOSITION ID IS D_1000039168. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 100 MM KCL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2 MM POL ETA UBZ; U-15N; 25 MM REMARK 210 PHOSPHATE, 100 MM KCL, 95% H20, REMARK 210 5% D20, 2 MM DTT; 2 MM POL ETA REMARK 210 UBZ; U-15N, 13C; 25 MM PHOSPHATE, REMARK 210 100 MM KCL, 95% H20, 5% D20, 2 REMARK 210 MM DTT; 2 MM POL ETA UBZ; 10%- REMARK 210 13C; 25 MM PHOSPHATE, 100 MM KCL, REMARK 210 95% H20, 5% D20, 2 MM DTT; 2 MM REMARK 210 POL ETA UBZ; U-15N, 13C; 25 MM REMARK 210 PHOSPHATE, 100 MM KCL, 100% D20, REMARK 210 2 MM DTT REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY; TRIPLE REMARK 210 RESONANCE EXPERIMENTS; 13C HSQC; REMARK 210 HCCH-TOCSY; RDC EXPERIMENTS REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 2.3, XEASY/CARA 1.5.1 REMARK 210 METHOD USED : STRUCTURE ORIGINALLY CALCULATED REMARK 210 BY TORSION ANGLE DYNAMICS AND REMARK 210 REFINED BY WATER REFINEMENT. REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 30 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL 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 1-15 REMARK 465 RES C SSSEQI REMARK 465 GLY A 1 REMARK 465 SER A 2 REMARK 465 HIS A 3 REMARK 465 MET A 4 REMARK 465 ALA A 5 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 2 CYS A 15 -23.68 -142.75 REMARK 500 3 CYS A 15 -10.94 -141.80 REMARK 500 4 GLU A 7 -37.98 68.94 REMARK 500 4 CYS A 15 -26.03 -142.33 REMARK 500 5 ASP A 8 55.82 -93.58 REMARK 500 5 CYS A 15 -15.63 -142.57 REMARK 500 5 LYS A 38 -34.08 -139.44 REMARK 500 6 CYS A 15 -20.29 -142.04 REMARK 500 6 LYS A 38 -50.11 -156.93 REMARK 500 7 GLU A 7 67.08 62.66 REMARK 500 7 CYS A 15 -21.17 -143.31 REMARK 500 8 ASP A 8 39.16 -93.27 REMARK 500 8 CYS A 15 -25.15 -141.92 REMARK 500 9 CYS A 15 -21.18 -143.64 REMARK 500 10 CYS A 15 -27.87 -140.83 REMARK 500 11 ASP A 8 56.69 -93.40 REMARK 500 11 CYS A 15 -23.22 -142.67 REMARK 500 12 LYS A 38 -21.11 62.54 REMARK 500 13 CYS A 15 -22.89 -143.53 REMARK 500 14 CYS A 15 -20.99 -142.95 REMARK 500 14 LYS A 38 2.54 53.42 REMARK 500 15 GLU A 7 33.77 -76.08 REMARK 500 15 CYS A 15 -25.70 -143.42 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HELIX REMARK 600 DETERMINATION METHOD: AUTHOR PROVIDED 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 336 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 12 SG REMARK 620 2 CYS A 15 SG 102.7 REMARK 620 3 HIS A 27 NE2 103.7 114.0 REMARK 620 4 HIS A 31 NE2 105.1 119.3 110.1 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 336 DBREF 2I5O A 5 39 UNP Q9Y253 POLH_HUMAN 628 662 SEQADV 2I5O GLY A 1 UNP Q9Y253 CLONING ARTIFACT SEQADV 2I5O SER A 2 UNP Q9Y253 CLONING ARTIFACT SEQADV 2I5O HIS A 3 UNP Q9Y253 CLONING ARTIFACT SEQADV 2I5O MET A 4 UNP Q9Y253 CLONING ARTIFACT SEQRES 1 A 39 GLY SER HIS MET ALA ALA GLU ASP GLN VAL PRO CYS GLU SEQRES 2 A 39 LYS CYS GLY SER LEU VAL PRO VAL TRP ASP MET PRO GLU SEQRES 3 A 39 HIS MET ASP TYR HIS PHE ALA LEU GLU LEU GLN LYS SER HET ZN A 336 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ HELIX 1 1 MET A 24 GLU A 35 1 12 SHEET 1 A 2 GLN A 9 PRO A 11 0 SHEET 2 A 2 LEU A 18 PRO A 20 -1 O VAL A 19 N VAL A 10 LINK SG CYS A 12 ZN ZN A 336 1555 1555 2.23 LINK SG CYS A 15 ZN ZN A 336 1555 1555 2.30 LINK NE2 HIS A 27 ZN ZN A 336 1555 1555 2.05 LINK NE2 HIS A 31 ZN ZN A 336 1555 1555 2.09 SITE 1 AC1 4 CYS A 12 CYS A 15 HIS A 27 HIS A 31 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