HEADER PROTEIN BINDING 29-MAR-06 2DIF TITLE ONE SEQUENCE TWO FOLD ? : MISS FOLD OF THE ZF-B-BOX DOMAIN FROM HUMAN TITLE 2 TRIPARTITE MOTIF PROTEIN 39 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRIPARTITE MOTIF PROTEIN 39; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ZF-B-BOX DOMAIN; COMPND 5 SYNONYM: RING FINGER PROTEIN 23, TESTIS-ABUNDANT FINGER PROTEIN; 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: TRIM39; SOURCE 6 EXPRESSION_SYSTEM: CELL FREE SYNTHESIS; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: P050302-55; SOURCE 9 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS KEYWDS ZF-B-BOX DOMIAN, ZN BINDING, ONE SEQUENCE TWO FOLD, NPPSFA, NATIONAL KEYWDS 2 PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES, STRUCTURAL KEYWDS 3 GENOMICS, RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, KEYWDS 4 PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR T.TOMIZAWA,S.KOSHIBA,M.INOUE,T.KIGAWA,S.YOKOYAMA,RIKEN STRUCTURAL AUTHOR 2 GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 3 09-MAR-22 2DIF 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 2DIF 1 VERSN REVDAT 1 29-SEP-06 2DIF 0 JRNL AUTH T.TOMIZAWA,S.KOSHIBA,M.INOUE,T.KIGAWA,S.YOKOYAMA JRNL TITL ONE SEQUENCE TWO FOLD ? : MISS FOLD OF THE ZF-B-BOX DOMAIN JRNL TITL 2 FROM HUMAN TRIPARTITE MOTIF PROTEIN 39 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 2.6, CYANA 2.0.17 REMARK 3 AUTHORS : BRUKER (XWINNMR), GUNTERT, P. (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2DIF COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-APR-06. REMARK 100 THE DEPOSITION ID IS D_1000025451. 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 ZF-B-BOX DOMAIN U-15N, REMARK 210 13C; 20MM D-TRIS-HCL(PH 7.0); REMARK 210 100MM NACL; 1MM D-DTT; 0.02% REMARK 210 NAN3; 50UM ZNCL2; 1MM IDA; 90% REMARK 210 H2O, 10% D2O 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 0.9742, CYANA 2.0.17 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 RESTRAINTED MOLECULAR 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 LOWEST ENERGY, STRUCTURES REMARK 210 WITH THE LEAST RESTRAINT REMARK 210 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 GLU A 8 154.91 -42.96 REMARK 500 1 ALA A 17 120.60 -39.54 REMARK 500 1 GLN A 26 31.84 70.14 REMARK 500 2 GLN A 13 -51.66 -127.93 REMARK 500 2 GLN A 26 28.50 49.59 REMARK 500 2 ALA A 41 36.41 71.67 REMARK 500 2 SER A 48 -26.30 -39.86 REMARK 500 3 LEU A 47 -63.63 -93.45 REMARK 500 4 PRO A 12 0.52 -69.77 REMARK 500 4 SER A 48 26.85 38.66 REMARK 500 5 SER A 6 117.80 -37.61 REMARK 500 5 SER A 48 31.42 -90.96 REMARK 500 6 GLN A 13 -48.36 -130.25 REMARK 500 6 ALA A 17 108.35 -49.16 REMARK 500 6 ARG A 40 39.35 -82.34 REMARK 500 7 SER A 19 31.26 -91.23 REMARK 500 7 ARG A 40 37.39 -85.32 REMARK 500 7 SER A 48 27.72 39.25 REMARK 500 7 SER A 51 108.17 -52.59 REMARK 500 8 SER A 3 176.51 -54.25 REMARK 500 8 PRO A 12 2.34 -69.73 REMARK 500 8 GLN A 13 -47.71 -131.35 REMARK 500 8 SER A 19 -32.62 -132.55 REMARK 500 8 LEU A 47 -63.74 -96.32 REMARK 500 8 SER A 51 -61.21 -98.02 REMARK 500 9 SER A 5 43.23 -87.39 REMARK 500 9 PRO A 12 3.60 -69.82 REMARK 500 9 GLN A 13 -41.18 -131.75 REMARK 500 9 THR A 38 -39.94 -38.81 REMARK 500 9 SER A 48 33.56 -87.91 REMARK 500 9 SER A 51 104.26 -51.58 REMARK 500 10 SER A 5 114.93 -161.13 REMARK 500 10 GLN A 26 36.15 35.85 REMARK 500 10 PRO A 50 -174.72 -69.79 REMARK 500 10 SER A 52 42.35 -96.65 REMARK 500 11 SER A 2 -55.64 -124.55 REMARK 500 11 SER A 48 25.67 47.05 REMARK 500 12 ALA A 17 131.55 -39.50 REMARK 500 12 SER A 19 41.74 -103.92 REMARK 500 12 GLN A 26 42.78 34.76 REMARK 500 12 LEU A 47 -60.87 -97.45 REMARK 500 12 SER A 48 -30.76 -39.73 REMARK 500 13 SER A 6 151.75 -35.90 REMARK 500 13 SER A 9 137.37 -171.40 REMARK 500 13 ALA A 17 123.48 -35.31 REMARK 500 13 SER A 19 37.09 -98.16 REMARK 500 13 ARG A 40 41.45 -81.36 REMARK 500 13 ALA A 41 45.18 37.56 REMARK 500 13 PRO A 50 89.03 -69.76 REMARK 500 14 SER A 5 107.39 -161.69 REMARK 500 REMARK 500 THIS ENTRY HAS 83 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 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 11 SG REMARK 620 2 HIS A 14 ND1 108.3 REMARK 620 3 CYS A 30 SG 121.4 100.7 REMARK 620 4 CYS A 33 SG 114.7 101.5 107.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 22 SG REMARK 620 2 ASP A 25 OD1 93.8 REMARK 620 3 ASP A 25 OD2 82.9 20.2 REMARK 620 4 HIS A 37 ND1 106.7 128.6 116.1 REMARK 620 5 HIS A 42 ND1 119.7 76.4 96.6 126.0 REMARK 620 N 1 2 3 4 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 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2DID RELATED DB: PDB REMARK 900 CORRECTLY FOLDED STRUCTURE OF ZF-B-BOX DOMAIN FROM HUMAN TRIPARTITE REMARK 900 MOTIF PROTEIN 39 REMARK 900 RELATED ID: HSI002005913.1 RELATED DB: TARGETDB DBREF 2DIF A 8 47 UNP Q9HCM9 TRI39_HUMAN 104 143 SEQADV 2DIF GLY A 1 UNP Q9HCM9 CLONING ARTIFACT SEQADV 2DIF SER A 2 UNP Q9HCM9 CLONING ARTIFACT SEQADV 2DIF SER A 3 UNP Q9HCM9 CLONING ARTIFACT SEQADV 2DIF GLY A 4 UNP Q9HCM9 CLONING ARTIFACT SEQADV 2DIF SER A 5 UNP Q9HCM9 CLONING ARTIFACT SEQADV 2DIF SER A 6 UNP Q9HCM9 CLONING ARTIFACT SEQADV 2DIF GLY A 7 UNP Q9HCM9 CLONING ARTIFACT SEQADV 2DIF SER A 48 UNP Q9HCM9 CLONING ARTIFACT SEQADV 2DIF GLY A 49 UNP Q9HCM9 CLONING ARTIFACT SEQADV 2DIF PRO A 50 UNP Q9HCM9 CLONING ARTIFACT SEQADV 2DIF SER A 51 UNP Q9HCM9 CLONING ARTIFACT SEQADV 2DIF SER A 52 UNP Q9HCM9 CLONING ARTIFACT SEQADV 2DIF GLY A 53 UNP Q9HCM9 CLONING ARTIFACT SEQRES 1 A 53 GLY SER SER GLY SER SER GLY GLU SER LEU CYS PRO GLN SEQRES 2 A 53 HIS HIS GLU ALA LEU SER LEU PHE CYS TYR GLU ASP GLN SEQRES 3 A 53 GLU ALA VAL CYS LEU ILE CYS ALA ILE SER HIS THR HIS SEQRES 4 A 53 ARG ALA HIS THR VAL VAL PRO LEU SER GLY PRO SER SER SEQRES 5 A 53 GLY HET ZN A 201 1 HET ZN A 401 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) HELIX 1 1 CYS A 30 ARG A 40 1 11 SHEET 1 A 3 GLU A 27 VAL A 29 0 SHEET 2 A 3 LEU A 20 CYS A 22 -1 N CYS A 22 O GLU A 27 SHEET 3 A 3 VAL A 44 VAL A 45 -1 O VAL A 45 N PHE A 21 LINK SG CYS A 11 ZN ZN A 201 1555 1555 2.30 LINK ND1 HIS A 14 ZN ZN A 201 1555 1555 2.10 LINK SG CYS A 22 ZN ZN A 401 1555 1555 2.23 LINK OD1 ASP A 25 ZN ZN A 401 1555 1555 4.01 LINK OD2 ASP A 25 ZN ZN A 401 1555 1555 2.06 LINK SG CYS A 30 ZN ZN A 201 1555 1555 2.24 LINK SG CYS A 33 ZN ZN A 201 1555 1555 2.34 LINK ND1 HIS A 37 ZN ZN A 401 1555 1555 1.91 LINK ND1 HIS A 42 ZN ZN A 401 1555 1555 2.04 SITE 1 AC1 4 CYS A 11 HIS A 14 CYS A 30 CYS A 33 SITE 1 AC2 4 CYS A 22 ASP A 25 HIS A 37 HIS A 42 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