HEADER TRANSCRIPTION 29-AUG-00 1FP0 TITLE SOLUTION STRUCTURE OF THE PHD DOMAIN FROM THE KAP-1 TITLE 2 COREPRESSOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: KAP-1 COREPRESSOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PHD DOMAIN; COMPND 5 SYNONYM: TRANSCRIPTION INTERMEDIARY FACTOR 1-BETA, NUCLEAR COMPND 6 COREPRESSOR, KAP-1, KRAB-ASSOCIATED PROTEIN 1; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PQE50 KEYWDS PHD DOMAIN, C3HC4 TYPE ZINC BINDING DOMAIN, NMR-STRUCTURE, KEYWDS 2 TRANSCRIPTION EXPDTA SOLUTION NMR AUTHOR A.D.CAPILI,D.C.SCHULTZ,F.J.RAUSCHER III,K.L.B.BORDEN REVDAT 3 24-FEB-09 1FP0 1 VERSN REVDAT 2 01-APR-03 1FP0 1 JRNL REVDAT 1 24-JAN-01 1FP0 0 JRNL AUTH A.D.CAPILI,D.C.SCHULTZ,F.J.RAUSCHERIII,K.L.BORDEN JRNL TITL SOLUTION STRUCTURE OF THE PHD DOMAIN FROM THE JRNL TITL 2 KAP-1 COREPRESSOR: STRUCTURAL DETERMINANTS FOR JRNL TITL 3 PHD, RING AND LIM ZINC-BINDING DOMAINS. JRNL REF EMBO J. V. 20 165 2001 JRNL REFN ISSN 0261-4189 JRNL PMID 11226167 JRNL DOI 10.1093/EMBOJ/20.1.165 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1FP0 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-SEP-00. REMARK 100 THE RCSB ID CODE IS RCSB011783. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 7.50 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.5-3.0 MM 15N-LABELLED OR REMARK 210 UNLABELLED KAP-1 PHD, 20 MM REMARK 210 NAH2PO4, 500 MM NACL, 5 MM REMARK 210 DTT, PH 7.5; 1.5-3.0 MM REMARK 210 UNLABELLED KAP-1 PHD, 20 MM REMARK 210 NAH2PO4, 500 MM NACL, 5 MM REMARK 210 DTT, PH 7.5 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : DISTANCE GEOMETRY AND REMARK 210 SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: FIRST 17 RESIDUES (MRGSHHHHHHGSDIIDE) AND LAST 9 REMARK 210 RESIDUES (VDLQACKLN) DO NOT BELONG TO THE NATURAL PROTEIN REMARK 210 MOLECULE, RESIDUES 618 TO 679 CORRESPONDS TO KAP-1, STRUCTURED REMARK 210 REGION CORRESPONDS TO RESIDUES 627-670 WHICH CONTAIN THE PHD REMARK 210 DOMAIN 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 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 SER A 4 30.42 -163.05 REMARK 500 HIS A 8 175.68 55.89 REMARK 500 HIS A 9 -143.53 -146.37 REMARK 500 HIS A 10 -82.44 -41.93 REMARK 500 ASP A 13 -50.47 178.08 REMARK 500 ILE A 14 -24.91 80.02 REMARK 500 ILE A 15 121.06 57.47 REMARK 500 THR A 20 34.63 38.56 REMARK 500 LEU A 21 -71.38 -139.57 REMARK 500 ASP A 22 -150.67 -81.86 REMARK 500 ASP A 23 19.81 55.51 REMARK 500 SER A 24 178.38 178.03 REMARK 500 ALA A 25 -135.38 70.64 REMARK 500 THR A 26 170.30 -39.89 REMARK 500 CYS A 31 -41.12 -160.21 REMARK 500 LYS A 33 -66.55 -140.88 REMARK 500 ASP A 36 104.18 44.28 REMARK 500 LEU A 37 105.86 -168.35 REMARK 500 ASN A 41 5.58 -69.34 REMARK 500 CYS A 43 -84.51 -153.92 REMARK 500 GLU A 44 33.37 -175.95 REMARK 500 PHE A 47 -157.40 -139.06 REMARK 500 LEU A 49 9.08 -69.49 REMARK 500 HIS A 52 -87.31 -88.79 REMARK 500 PRO A 54 63.90 -63.22 REMARK 500 ALA A 55 42.52 177.18 REMARK 500 GLU A 62 -108.90 58.73 REMARK 500 GLU A 63 -151.36 -99.66 REMARK 500 TRP A 64 -102.24 -74.91 REMARK 500 SER A 65 37.42 172.62 REMARK 500 CYS A 66 163.62 57.50 REMARK 500 SER A 67 -141.70 -135.06 REMARK 500 VAL A 71 52.71 -111.23 REMARK 500 CYS A 85 -144.70 -59.14 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 ARG A 2 0.28 SIDE_CHAIN REMARK 500 ARG A 29 0.32 SIDE_CHAIN 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 89 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 40 SG REMARK 620 2 CYS A 43 SG 106.4 REMARK 620 3 CYS A 66 SG 111.0 110.2 REMARK 620 4 CYS A 69 SG 109.5 109.1 110.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 90 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 28 SG REMARK 620 2 CYS A 31 SG 112.0 REMARK 620 3 CYS A 51 SG 110.9 108.6 REMARK 620 4 HIS A 48 ND1 109.9 108.3 107.0 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 89 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 90 DBREF 1FP0 A 19 79 UNP Q13263 TIF1B_HUMAN 619 679 SEQADV 1FP0 MET A 1 UNP Q13263 EXPRESSION TAG SEQADV 1FP0 ARG A 2 UNP Q13263 EXPRESSION TAG SEQADV 1FP0 GLY A 3 UNP Q13263 EXPRESSION TAG SEQADV 1FP0 SER A 4 UNP Q13263 EXPRESSION TAG SEQADV 1FP0 HIS A 5 UNP Q13263 EXPRESSION TAG SEQADV 1FP0 HIS A 6 UNP Q13263 EXPRESSION TAG SEQADV 1FP0 HIS A 7 UNP Q13263 EXPRESSION TAG SEQADV 1FP0 HIS A 8 UNP Q13263 EXPRESSION TAG SEQADV 1FP0 HIS A 9 UNP Q13263 EXPRESSION TAG SEQADV 1FP0 HIS A 10 UNP Q13263 EXPRESSION TAG SEQADV 1FP0 GLY A 11 UNP Q13263 EXPRESSION TAG SEQADV 1FP0 SER A 12 UNP Q13263 EXPRESSION TAG SEQADV 1FP0 ASP A 13 UNP Q13263 EXPRESSION TAG SEQADV 1FP0 ILE A 14 UNP Q13263 EXPRESSION TAG SEQADV 1FP0 ILE A 15 UNP Q13263 EXPRESSION TAG SEQADV 1FP0 ASP A 16 UNP Q13263 EXPRESSION TAG SEQADV 1FP0 GLU A 17 UNP Q13263 EXPRESSION TAG SEQADV 1FP0 PHE A 18 UNP Q13263 EXPRESSION TAG SEQADV 1FP0 VAL A 80 UNP Q13263 CLONING ARTIFACT SEQADV 1FP0 ASP A 81 UNP Q13263 CLONING ARTIFACT SEQADV 1FP0 LEU A 82 UNP Q13263 CLONING ARTIFACT SEQADV 1FP0 GLN A 83 UNP Q13263 CLONING ARTIFACT SEQADV 1FP0 ALA A 84 UNP Q13263 CLONING ARTIFACT SEQADV 1FP0 CYS A 85 UNP Q13263 CLONING ARTIFACT SEQADV 1FP0 LYS A 86 UNP Q13263 CLONING ARTIFACT SEQADV 1FP0 LEU A 87 UNP Q13263 CLONING ARTIFACT SEQADV 1FP0 ASN A 88 UNP Q13263 CLONING ARTIFACT SEQRES 1 A 88 MET ARG GLY SER HIS HIS HIS HIS HIS HIS GLY SER ASP SEQRES 2 A 88 ILE ILE ASP GLU PHE GLY THR LEU ASP ASP SER ALA THR SEQRES 3 A 88 ILE CYS ARG VAL CYS GLN LYS PRO GLY ASP LEU VAL MET SEQRES 4 A 88 CYS ASN GLN CYS GLU PHE CYS PHE HIS LEU ASP CYS HIS SEQRES 5 A 88 LEU PRO ALA LEU GLN ASP VAL PRO GLY GLU GLU TRP SER SEQRES 6 A 88 CYS SER LEU CYS HIS VAL LEU PRO ASP LEU LYS GLU GLU SEQRES 7 A 88 ASP VAL ASP LEU GLN ALA CYS LYS LEU ASN HET ZN A 89 1 HET ZN A 90 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) SHEET 1 A 3 VAL A 38 CYS A 40 0 SHEET 2 A 3 PHE A 45 PHE A 47 -1 N PHE A 47 O VAL A 38 SHEET 3 A 3 TRP A 64 SER A 67 0 LINK ZN ZN A 89 SG CYS A 40 1555 1555 2.28 LINK ZN ZN A 89 SG CYS A 43 1555 1555 2.30 LINK ZN ZN A 89 SG CYS A 66 1555 1555 2.32 LINK ZN ZN A 89 SG CYS A 69 1555 1555 2.30 LINK ZN ZN A 90 SG CYS A 28 1555 1555 2.34 LINK ZN ZN A 90 SG CYS A 31 1555 1555 2.31 LINK ZN ZN A 90 SG CYS A 51 1555 1555 2.29 LINK ZN ZN A 90 ND1 HIS A 48 1555 1555 1.98 SITE 1 AC1 5 CYS A 40 GLN A 42 CYS A 43 CYS A 66 SITE 2 AC1 5 CYS A 69 SITE 1 AC2 6 CYS A 28 VAL A 30 CYS A 31 PHE A 47 SITE 2 AC2 6 HIS A 48 CYS A 51 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 MASTER 154 0 2 0 3 0 4 6 0 0 0 7 END