PDB Short entry for 2D9T HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 13-DEC-05 2D9T TITLE SOLUTION STRUCTURE OF THE TUDOR DOMAIN OF TUDOR DOMAIN CONTAINING TITLE 2 PROTEIN 3 FROM MOUSE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TUDOR DOMAIN-CONTAINING PROTEIN 3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: TUDOR DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: TDRD3; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: P050214-04; SOURCE 8 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS KEYWDS TUDOR DOMAIN, STRUCTURAL GENOMICS, NPPSFA, NATIONAL PROJECT ON KEYWDS 2 PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES, RIKEN STRUCTURAL KEYWDS 3 GENOMICS/PROTEOMICS INITIATIVE, RSGI, UNKNOWN FUNCTION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR H.LI,T.TOMIZAWA,S.KOSHIBA,M.INOUE,T.KIGAWA,S.YOKOYAMA,RIKEN AUTHOR 2 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 3 09-MAR-22 2D9T 1 REMARK SEQADV REVDAT 2 24-FEB-09 2D9T 1 VERSN REVDAT 1 13-JUN-06 2D9T 0 JRNL AUTH H.LI,T.TOMIZAWA,S.KOSHIBA,M.INOUE,T.KIGAWA,S.YOKOYAMA JRNL TITL SOLUTION STRUCTURE OF THE TUDOR DOMAIN OF TUDOR DOMAIN JRNL TITL 2 CONTAINING PROTEIN 3 FROM MOUSE 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 2D9T COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-DEC-05. REMARK 100 THE DEPOSITION ID IS D_1000025164. 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 : 1.22MM TUDOR DOMAIN U-15N, 13C; REMARK 210 20MM D-TRIS-HCL(PH 7.0); 100MM REMARK 210 NACL; 1MM D-DTT; 0.02% NAN3; 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 0.932, 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 PRO A 12 99.78 -69.77 REMARK 500 1 ALA A 29 -176.41 -170.73 REMARK 500 1 VAL A 31 100.27 -54.45 REMARK 500 1 MET A 39 -56.86 -132.20 REMARK 500 1 TYR A 48 -39.92 -132.70 REMARK 500 1 ALA A 66 41.75 -91.31 REMARK 500 1 ASP A 70 141.15 -173.08 REMARK 500 2 SER A 2 41.58 -108.45 REMARK 500 2 SER A 5 40.09 -91.10 REMARK 500 2 ASP A 23 -35.24 -131.79 REMARK 500 2 VAL A 31 104.89 -46.22 REMARK 500 2 SER A 37 -71.65 -71.20 REMARK 500 2 MET A 39 -59.95 -133.75 REMARK 500 2 TYR A 48 -41.39 -133.85 REMARK 500 2 GLU A 65 39.35 -91.50 REMARK 500 2 ALA A 66 43.79 -92.75 REMARK 500 2 SER A 73 42.39 -103.52 REMARK 500 3 SER A 6 41.49 36.00 REMARK 500 3 PRO A 12 95.17 -69.83 REMARK 500 3 TYR A 48 -44.46 -134.15 REMARK 500 3 PRO A 71 -172.19 -69.84 REMARK 500 3 PRO A 75 89.02 -69.77 REMARK 500 4 VAL A 31 106.18 -46.73 REMARK 500 4 SER A 37 -65.29 -94.93 REMARK 500 4 MET A 39 -58.93 -126.44 REMARK 500 4 ALA A 66 42.78 -86.02 REMARK 500 4 TRP A 67 91.96 -50.83 REMARK 500 4 SER A 76 -48.75 -132.59 REMARK 500 5 VAL A 31 100.90 -57.51 REMARK 500 5 ALA A 33 132.97 -172.20 REMARK 500 5 GLN A 63 147.50 -35.20 REMARK 500 5 ALA A 66 42.94 -92.78 REMARK 500 5 TRP A 67 132.98 -38.19 REMARK 500 5 ARG A 69 101.35 -45.37 REMARK 500 5 PRO A 71 -179.72 -69.78 REMARK 500 6 VAL A 31 103.75 -46.83 REMARK 500 6 GLN A 63 119.60 -36.98 REMARK 500 6 ALA A 66 47.93 -104.56 REMARK 500 6 PRO A 71 -173.67 -69.80 REMARK 500 7 SER A 2 -43.33 -131.35 REMARK 500 7 SER A 5 103.97 -53.79 REMARK 500 7 TYR A 48 -41.26 -134.43 REMARK 500 7 GLN A 63 141.27 -34.67 REMARK 500 7 THR A 64 175.63 -58.61 REMARK 500 7 ALA A 66 36.01 38.01 REMARK 500 7 VAL A 68 114.46 -35.28 REMARK 500 7 SER A 76 40.01 71.40 REMARK 500 8 SER A 37 -71.74 -50.23 REMARK 500 8 GLU A 65 82.21 -68.06 REMARK 500 8 ALA A 66 51.20 -116.84 REMARK 500 REMARK 500 THIS ENTRY HAS 121 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR DETERMINED REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: MMT008000619.1 RELATED DB: TARGETDB DBREF 2D9T A 8 67 UNP Q91W18 TDRD3_MOUSE 553 612 SEQADV 2D9T GLY A 1 UNP Q91W18 CLONING ARTIFACT SEQADV 2D9T SER A 2 UNP Q91W18 CLONING ARTIFACT SEQADV 2D9T SER A 3 UNP Q91W18 CLONING ARTIFACT SEQADV 2D9T GLY A 4 UNP Q91W18 CLONING ARTIFACT SEQADV 2D9T SER A 5 UNP Q91W18 CLONING ARTIFACT SEQADV 2D9T SER A 6 UNP Q91W18 CLONING ARTIFACT SEQADV 2D9T GLY A 7 UNP Q91W18 CLONING ARTIFACT SEQADV 2D9T VAL A 68 UNP Q91W18 CLONING ARTIFACT SEQADV 2D9T ARG A 69 UNP Q91W18 CLONING ARTIFACT SEQADV 2D9T ASP A 70 UNP Q91W18 CLONING ARTIFACT SEQADV 2D9T PRO A 71 UNP Q91W18 CLONING ARTIFACT SEQADV 2D9T ASN A 72 UNP Q91W18 CLONING ARTIFACT SEQADV 2D9T SER A 73 UNP Q91W18 CLONING ARTIFACT SEQADV 2D9T GLY A 74 UNP Q91W18 CLONING ARTIFACT SEQADV 2D9T PRO A 75 UNP Q91W18 CLONING ARTIFACT SEQADV 2D9T SER A 76 UNP Q91W18 CLONING ARTIFACT SEQADV 2D9T SER A 77 UNP Q91W18 CLONING ARTIFACT SEQADV 2D9T GLY A 78 UNP Q91W18 CLONING ARTIFACT SEQRES 1 A 78 GLY SER SER GLY SER SER GLY LYS VAL TRP LYS PRO GLY SEQRES 2 A 78 ASP GLU CYS PHE ALA LEU TYR TRP GLU ASP ASN LYS PHE SEQRES 3 A 78 TYR ARG ALA GLU VAL GLU ALA LEU HIS SER SER GLY MET SEQRES 4 A 78 THR ALA VAL VAL LYS PHE THR ASP TYR GLY ASN TYR GLU SEQRES 5 A 78 GLU VAL LEU LEU SER ASN ILE LYS PRO VAL GLN THR GLU SEQRES 6 A 78 ALA TRP VAL ARG ASP PRO ASN SER GLY PRO SER SER GLY HELIX 1 1 LEU A 56 ASN A 58 1 3 SHEET 1 A 5 TYR A 51 LEU A 55 0 SHEET 2 A 5 THR A 40 PHE A 45 -1 N ALA A 41 O VAL A 54 SHEET 3 A 5 PHE A 26 LEU A 34 -1 N ALA A 33 O VAL A 42 SHEET 4 A 5 GLU A 15 LEU A 19 -1 N ALA A 18 O TYR A 27 SHEET 5 A 5 ILE A 59 PRO A 61 -1 O LYS A 60 N PHE A 17 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