HEADER TRANSCRIPTION 21-APR-06 2DMD TITLE SOLUTION STRUCTURE OF THE N-TERMINAL C2H2 TYPE ZINC-BINDING DOMAIN OF TITLE 2 THE ZINC FINGER PROTEIN 64, ISOFORMS 1 AND 2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ZINC FINGER PROTEIN 64, ISOFORMS 1 AND 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C2H2-TYPE ZINC-BINDING DOMAIN; COMPND 5 SYNONYM: ZINC FINGER PROTEIN 338; 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: ZFP64; SOURCE 6 EXPRESSION_SYSTEM: CELL FREE SYNTHESIS; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: P050815-12; SOURCE 9 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS KEYWDS ZINC FINGER PROTEIN 338, ZNF338, NUCLEAR PROTEIN, DNA-BINDING, KEYWDS 2 TRANSCRIPTION, C2H2-TYPE ZINC FINGER, STRUCTURAL GENOMICS, NPPSFA, KEYWDS 3 NATIONAL PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES, KEYWDS 4 RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.YONEYAMA,N.TOCHIO,S.KOSHIBA,M.INOUE,T.KIGAWA,S.YOKOYAMA,RIKEN AUTHOR 2 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 3 09-MAR-22 2DMD 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 2DMD 1 VERSN REVDAT 1 21-OCT-06 2DMD 0 JRNL AUTH M.YONEYAMA,N.TOCHIO,S.KOSHIBA,M.INOUE,T.KIGAWA,S.YOKOYAMA JRNL TITL SOLUTION STRUCTURE OF THE N-TERMINAL C2H2 TYPE ZINC-BINDING JRNL TITL 2 DOMAIN OF THE ZINC FINGER PROTEIN 64, ISOFORMS 1 AND 2 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 3.5, CYANA 2.0.17 REMARK 3 AUTHORS : BRUKER (XWINNMR), GUNTERT, P. (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2DMD COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-APR-06. REMARK 100 THE DEPOSITION ID IS D_1000025584. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 296 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 120MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.28MM C2H2 TYPE ZINC-BINDING REMARK 210 DOMAIN U-15N, 13C; 20MM D-TRIS REMARK 210 HCL(PH7.0); 100MM NACL; 1MM D- REMARK 210 DTT; 0.02% NAN3; 50UM ZNCL2 + REMARK 210 1MM IDA; 10% D2O, 90% H2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 20030801, NMRVIEW 5.0.4, REMARK 210 KUJIRA 0.9736, CYANA 2.0.17 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION, STRUCTURES WITH REMARK 210 THE LEAST RESTRAINT VIOLATIONS 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 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 LYS A 25 -37.43 -35.19 REMARK 500 1 ARG A 29 -36.02 -35.76 REMARK 500 1 THR A 32 79.59 -119.89 REMARK 500 1 VAL A 34 57.72 -96.28 REMARK 500 1 PRO A 71 4.19 -69.81 REMARK 500 1 HIS A 87 86.04 -64.00 REMARK 500 1 SER A 94 115.03 -170.82 REMARK 500 2 PRO A 8 -164.33 -69.79 REMARK 500 2 ASP A 61 -37.06 -35.88 REMARK 500 2 GLU A 62 -74.35 -40.23 REMARK 500 2 PRO A 71 3.25 -69.73 REMARK 500 2 TYR A 72 167.90 -43.68 REMARK 500 2 ARG A 75 41.22 -85.44 REMARK 500 2 SER A 94 128.01 -39.14 REMARK 500 3 CYS A 11 178.82 -52.79 REMARK 500 3 GLU A 12 -41.59 -131.49 REMARK 500 3 PRO A 71 3.10 -69.72 REMARK 500 3 TYR A 72 168.32 -44.71 REMARK 500 3 HIS A 87 80.84 -65.58 REMARK 500 4 CYS A 11 171.71 -49.82 REMARK 500 4 HIS A 31 64.79 -107.71 REMARK 500 4 THR A 32 61.29 -109.24 REMARK 500 4 LYS A 35 73.46 -113.09 REMARK 500 4 TYR A 37 91.12 -65.58 REMARK 500 4 THR A 41 -61.95 -91.03 REMARK 500 4 ALA A 47 32.20 -92.27 REMARK 500 4 PRO A 71 2.22 -69.78 REMARK 500 5 SER A 3 139.17 -174.86 REMARK 500 5 PRO A 8 -175.29 -69.72 REMARK 500 5 HIS A 27 -28.90 -38.04 REMARK 500 5 LYS A 35 94.30 -30.28 REMARK 500 5 HIS A 59 -176.37 -63.03 REMARK 500 5 SER A 60 25.51 41.33 REMARK 500 5 ASP A 61 42.89 34.57 REMARK 500 5 GLU A 62 142.55 -36.57 REMARK 500 5 PRO A 71 7.05 -69.77 REMARK 500 5 TYR A 72 151.80 -49.73 REMARK 500 5 THR A 88 -53.56 -125.48 REMARK 500 6 SER A 3 148.56 -173.72 REMARK 500 6 PRO A 8 -168.21 -69.80 REMARK 500 6 HIS A 27 -37.27 -35.93 REMARK 500 6 THR A 41 -63.68 -91.92 REMARK 500 6 GLU A 62 172.24 -55.23 REMARK 500 6 PRO A 71 4.57 -69.80 REMARK 500 6 TYR A 72 168.50 -44.80 REMARK 500 6 ASN A 76 177.33 -57.56 REMARK 500 6 HIS A 87 86.37 -65.56 REMARK 500 7 HIS A 31 35.86 -88.16 REMARK 500 7 THR A 32 121.07 -171.25 REMARK 500 7 ILE A 58 -39.42 -33.46 REMARK 500 REMARK 500 THIS ENTRY HAS 179 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL 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 191 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 11 SG REMARK 620 2 CYS A 14 SG 105.3 REMARK 620 3 HIS A 27 NE2 96.4 117.6 REMARK 620 4 HIS A 31 NE2 112.7 113.8 109.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 241 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 39 SG REMARK 620 2 CYS A 42 SG 104.7 REMARK 620 3 HIS A 55 NE2 103.3 114.5 REMARK 620 4 HIS A 59 NE2 117.4 105.7 111.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 291 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 67 SG REMARK 620 2 CYS A 70 SG 106.1 REMARK 620 3 HIS A 83 NE2 97.7 101.4 REMARK 620 4 HIS A 87 NE2 106.4 126.3 115.1 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 191 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 241 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 291 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1X5W RELATED DB: PDB REMARK 900 THE DIFFERENT FRAGMENT FROM THE SAME PROTEIN REMARK 900 RELATED ID: HSS001003730.2 RELATED DB: TARGETDB DBREF 2DMD A 8 90 UNP Q9NPA5 ZF64A_HUMAN 174 256 SEQADV 2DMD GLY A 1 UNP Q9NPA5 CLONING ARTIFACT SEQADV 2DMD SER A 2 UNP Q9NPA5 CLONING ARTIFACT SEQADV 2DMD SER A 3 UNP Q9NPA5 CLONING ARTIFACT SEQADV 2DMD GLY A 4 UNP Q9NPA5 CLONING ARTIFACT SEQADV 2DMD SER A 5 UNP Q9NPA5 CLONING ARTIFACT SEQADV 2DMD SER A 6 UNP Q9NPA5 CLONING ARTIFACT SEQADV 2DMD GLY A 7 UNP Q9NPA5 CLONING ARTIFACT SEQADV 2DMD SER A 91 UNP Q9NPA5 CLONING ARTIFACT SEQADV 2DMD GLY A 92 UNP Q9NPA5 CLONING ARTIFACT SEQADV 2DMD PRO A 93 UNP Q9NPA5 CLONING ARTIFACT SEQADV 2DMD SER A 94 UNP Q9NPA5 CLONING ARTIFACT SEQADV 2DMD SER A 95 UNP Q9NPA5 CLONING ARTIFACT SEQADV 2DMD GLY A 96 UNP Q9NPA5 CLONING ARTIFACT SEQRES 1 A 96 GLY SER SER GLY SER SER GLY PRO HIS LYS CYS GLU VAL SEQRES 2 A 96 CYS GLY LYS CYS PHE SER ARG LYS ASP LYS LEU LYS THR SEQRES 3 A 96 HIS MET ARG CYS HIS THR GLY VAL LYS PRO TYR LYS CYS SEQRES 4 A 96 LYS THR CYS ASP TYR ALA ALA ALA ASP SER SER SER LEU SEQRES 5 A 96 ASN LYS HIS LEU ARG ILE HIS SER ASP GLU ARG PRO PHE SEQRES 6 A 96 LYS CYS GLN ILE CYS PRO TYR ALA SER ARG ASN SER SER SEQRES 7 A 96 GLN LEU THR VAL HIS LEU ARG SER HIS THR GLY ASP SER SEQRES 8 A 96 GLY PRO SER SER GLY HET ZN A 191 1 HET ZN A 241 1 HET ZN A 291 1 HETNAM ZN ZINC ION FORMUL 2 ZN 3(ZN 2+) HELIX 1 1 ARG A 20 MET A 28 1 9 HELIX 2 2 ARG A 29 HIS A 31 5 3 HELIX 3 3 ASP A 48 HIS A 59 1 12 HELIX 4 4 ASN A 76 ARG A 85 1 10 SHEET 1 A 2 TYR A 37 LYS A 38 0 SHEET 2 A 2 ALA A 45 ALA A 46 -1 O ALA A 46 N TYR A 37 SHEET 1 B 2 PHE A 65 LYS A 66 0 SHEET 2 B 2 ALA A 73 SER A 74 -1 O SER A 74 N PHE A 65 LINK SG CYS A 11 ZN ZN A 191 1555 1555 2.39 LINK SG CYS A 14 ZN ZN A 191 1555 1555 2.20 LINK NE2 HIS A 27 ZN ZN A 191 1555 1555 2.07 LINK NE2 HIS A 31 ZN ZN A 191 1555 1555 2.02 LINK SG CYS A 39 ZN ZN A 241 1555 1555 2.24 LINK SG CYS A 42 ZN ZN A 241 1555 1555 2.37 LINK NE2 HIS A 55 ZN ZN A 241 1555 1555 2.01 LINK NE2 HIS A 59 ZN ZN A 241 1555 1555 2.00 LINK SG CYS A 67 ZN ZN A 291 1555 1555 2.35 LINK SG CYS A 70 ZN ZN A 291 1555 1555 2.19 LINK NE2 HIS A 83 ZN ZN A 291 1555 1555 2.10 LINK NE2 HIS A 87 ZN ZN A 291 1555 1555 1.96 SITE 1 AC1 5 CYS A 11 VAL A 13 CYS A 14 HIS A 27 SITE 2 AC1 5 HIS A 31 SITE 1 AC2 4 CYS A 39 CYS A 42 HIS A 55 HIS A 59 SITE 1 AC3 4 CYS A 67 CYS A 70 HIS A 83 HIS A 87 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