PDB Short entry for 2KDP HEADER TRANSCRIPTION 14-JAN-09 2KDP TITLE SOLUTION STRUCTURE OF THE SAP30 ZINC FINGER MOTIF COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE DEACETYLASE COMPLEX SUBUNIT SAP30; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SIN3-ASSOCIATED POLYPEPTIDE, 30 KDA, SIN3 COREPRESSOR COMPND 5 COMPLEX SUBUNIT SAP30; 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: SAP30; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PMCSG7 KEYWDS SAP30, SIN3, ZINC FINGER MOTIF, NUCLEIC ACID INTERACTION, NUCLEUS, KEYWDS 2 REPRESSOR, TRANSCRIPTION, TRANSCRIPTION REGULATION EXPDTA SOLUTION NMR NUMMDL 47 AUTHOR Y.HE,R.IMHOFF,A.SAHU,I.RADHAKRISHNAN REVDAT 3 19-FEB-20 2KDP 1 REMARK SEQADV REVDAT 2 12-MAY-09 2KDP 1 JRNL REVDAT 1 17-MAR-09 2KDP 0 JRNL AUTH Y.HE,R.IMHOFF,A.SAHU,I.RADHAKRISHNAN JRNL TITL SOLUTION STRUCTURE OF A NOVEL ZINC FINGER MOTIF IN THE SAP30 JRNL TITL 2 POLYPEPTIDE OF THE SIN3 COREPRESSOR COMPLEX AND ITS JRNL TITL 3 POTENTIAL ROLE IN NUCLEIC ACID RECOGNITION JRNL REF NUCLEIC ACIDS RES. V. 37 2142 2009 JRNL REFN ISSN 0305-1048 JRNL PMID 19223330 JRNL DOI 10.1093/NAR/GKP051 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMRJ, ARIA, CNS, PROCHECK, ISD 1.1 REMARK 3 AUTHORS : VARIAN (VNMRJ), LINGE, O'DONOGHUE AND NILGES REMARK 3 (ARIA), BRUNGER, ADAMS, CLORE, GROS, NILGES AND REMARK 3 READ (CNS), LASKOWSKI, MACARTHUR, SMITH, JONES, REMARK 3 HUTCHINSON, MORRIS, MOSS AND THO (PROCHECK), REMARK 3 RIEPING, HABECK, AND LAMAZHAPOVA (ISD) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURES WERE DETERMINED USING A REMARK 3 COMBINATION OF REPLICA-EXCHANGE MONTE CARLO AND BAYESIAN REMARK 3 INFERENCE USING THE INFERENTIAL STRUCTURE DETERMINATION PROGRAM REMARK 3 (ISD). NOE ASSIGNMENTS WERE MADE USING ARIA AND CNS. REMARK 4 REMARK 4 2KDP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-JAN-09. REMARK 100 THE DEPOSITION ID IS D_1000100992. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 0.04 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.56 MM [U-95% 13C; U-95% 15N] REMARK 210 SAP30 ZNF, 20 MM [U-13C; U-15N] REMARK 210 TRIS, 20 MM [U-13C] ACETIC ACID, REMARK 210 2 MM [U-2H] DTT, 0.2 % SODIUM REMARK 210 AZIDE, 0.56 MM ZINC CHLORIDE, 90% REMARK 210 H2O/10% D2O; 0.56 MM [U-95% 13C; REMARK 210 U-95% 15N] SAP30 ZNF, 20 MM [U- REMARK 210 13C; U-15N] TRIS, 20 MM [U-13C] REMARK 210 ACETIC ACID, 2 MM [U-2H] DTT, REMARK 210 0.2 % SODIUM AZIDE, 0.56 MM ZINC REMARK 210 CHLORIDE, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D CBCA(CO)NH; 3D HNCO; 3D REMARK 210 HNCACB; 3D H(CCO)NH; 3D HCCH- REMARK 210 TOCSY; 3D HCCH-COSY; 3D 1H-15N REMARK 210 NOESY; 3D 1H-13C NOESY 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 : FELIX, NMRVIEW, TALOS, ARIA, CNS REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 3000 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 47 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY AND IN GOOD REMARK 210 AGREEMENT WITH EXPERIMENTAL DATA 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE 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 ALA A 63 14.59 -157.21 REMARK 500 1 CYS A 76 -76.39 41.87 REMARK 500 1 SER A 86 -168.21 -115.21 REMARK 500 1 LYS A 97 74.61 60.84 REMARK 500 1 SER A 121 30.34 -85.09 REMARK 500 1 ASN A 124 92.79 -171.21 REMARK 500 1 ARG A 125 -38.61 -159.58 REMARK 500 1 LYS A 127 19.97 -149.66 REMARK 500 1 LYS A 129 -35.88 -163.03 REMARK 500 2 ALA A 63 16.18 -154.25 REMARK 500 2 CYS A 67 158.42 -46.92 REMARK 500 2 CYS A 76 -72.65 -58.00 REMARK 500 2 LYS A 97 61.58 63.78 REMARK 500 2 LYS A 99 43.57 -88.35 REMARK 500 2 SER A 121 47.50 -90.08 REMARK 500 2 ARG A 125 101.79 -163.16 REMARK 500 2 ARG A 128 -167.67 47.83 REMARK 500 2 LYS A 129 -81.27 -151.65 REMARK 500 3 ALA A 63 29.57 -141.34 REMARK 500 3 LYS A 99 40.90 -91.64 REMARK 500 3 ALA A 106 -165.91 -64.92 REMARK 500 3 LEU A 109 73.32 -110.86 REMARK 500 3 ARG A 128 175.40 63.47 REMARK 500 3 LYS A 129 -70.36 -169.44 REMARK 500 4 ASN A 62 70.83 60.80 REMARK 500 4 ALA A 63 22.10 -149.29 REMARK 500 4 CYS A 76 -82.94 44.61 REMARK 500 4 LYS A 97 75.73 67.88 REMARK 500 4 ALA A 106 152.99 -47.79 REMARK 500 4 LEU A 109 73.10 -116.81 REMARK 500 4 SER A 121 62.30 -110.78 REMARK 500 4 VAL A 122 -46.60 -132.28 REMARK 500 4 LYS A 127 -143.34 61.67 REMARK 500 4 ARG A 128 -45.98 -139.63 REMARK 500 4 LYS A 129 -85.62 55.51 REMARK 500 5 ALA A 63 36.33 -148.68 REMARK 500 5 ARG A 75 173.55 -58.48 REMARK 500 5 CYS A 76 -60.90 -92.61 REMARK 500 5 LYS A 97 74.86 53.65 REMARK 500 5 LYS A 99 55.44 -92.32 REMARK 500 5 ARG A 107 -43.84 -130.70 REMARK 500 5 ARG A 123 25.90 47.23 REMARK 500 5 ASN A 124 19.93 -157.56 REMARK 500 5 ARG A 126 -79.13 60.98 REMARK 500 5 LYS A 127 82.89 57.96 REMARK 500 5 ARG A 128 -168.83 -120.39 REMARK 500 6 ALA A 63 19.61 -157.56 REMARK 500 6 GLN A 65 -165.43 -109.63 REMARK 500 6 CYS A 68 41.07 -108.15 REMARK 500 6 ALA A 83 176.70 -58.98 REMARK 500 REMARK 500 THIS ENTRY HAS 443 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 1 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 67 SG REMARK 620 2 CYS A 76 SG 109.5 REMARK 620 3 CYS A 112 SG 107.8 94.6 REMARK 620 4 HIS A 115 ND1 108.0 121.1 114.8 REMARK 620 N 1 2 3 REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR 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 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 16127 RELATED DB: BMRB DBREF 2KDP A 64 131 UNP O75446 SAP30_HUMAN 64 131 SEQADV 2KDP SER A 61 UNP O75446 EXPRESSION TAG SEQADV 2KDP ASN A 62 UNP O75446 EXPRESSION TAG SEQADV 2KDP ALA A 63 UNP O75446 EXPRESSION TAG SEQRES 1 A 71 SER ASN ALA GLY GLN LEU CYS CYS LEU ARG GLU ASP GLY SEQRES 2 A 71 GLU ARG CYS GLY ARG ALA ALA GLY ASN ALA SER PHE SER SEQRES 3 A 71 LYS ARG ILE GLN LYS SER ILE SER GLN LYS LYS VAL LYS SEQRES 4 A 71 ILE GLU LEU ASP LYS SER ALA ARG HIS LEU TYR ILE CYS SEQRES 5 A 71 ASP TYR HIS LYS ASN LEU ILE GLN SER VAL ARG ASN ARG SEQRES 6 A 71 ARG LYS ARG LYS GLY SER HET ZN A 1 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ HELIX 1 1 LYS A 87 LYS A 96 1 10 HELIX 2 2 ASP A 113 GLN A 120 1 8 SHEET 1 A 2 LEU A 69 GLU A 71 0 SHEET 2 A 2 ILE A 100 LEU A 102 -1 O GLU A 101 N ARG A 70 LINK SG CYS A 67 ZN ZN A 1 1555 1555 2.30 LINK SG CYS A 76 ZN ZN A 1 1555 1555 2.30 LINK SG CYS A 112 ZN ZN A 1 1555 1555 2.30 LINK ND1 HIS A 115 ZN ZN A 1 1555 1555 1.98 SITE 1 AC1 5 CYS A 67 LEU A 69 CYS A 76 ARG A 78 SITE 2 AC1 5 CYS A 112 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