PDB Short entry for 2DH8 HEADER RNA BINDING PROTEIN 23-MAR-06 2DH8 TITLE SOLUTION STRUCTURE OF THE N-TERMINAL RNA BINDING DOMAIN IN DAZ- TITLE 2 ASSOCIATED PROTEIN 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DAZ-ASSOCIATED PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RNA RECOGNITION MOTIF; COMPND 5 SYNONYM: DELETED IN AZOOSPERMIA-ASSOCIATED PROTEIN 1; 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: DAZAP1; SOURCE 6 EXPRESSION_SYSTEM: CELL FREE SYNTHESIS; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: P050704-07; SOURCE 9 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS KEYWDS RRM DOMAIN, STRUCTURAL GENOMICS, NPPSFA, NATIONAL PROJECT ON PROTEIN KEYWDS 2 STRUCTURAL AND FUNCTIONAL ANALYSES, RIKEN STRUCTURAL KEYWDS 3 GENOMICS/PROTEOMICS INITIATIVE, RSGI, RNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR S.ARAI,K.TSUDA,Y.MUTO,M.INOUE,T.KIGAWA,T.TERADA,M.SHIROUZU, AUTHOR 2 S.YOKOYAMA,RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 3 09-MAR-22 2DH8 1 REMARK SEQADV REVDAT 2 24-FEB-09 2DH8 1 VERSN REVDAT 1 23-SEP-06 2DH8 0 JRNL AUTH S.ARAI,K.TSUDA,Y.MUTO,M.INOUE,T.KIGAWA,T.TERADA,M.SHIROUZU, JRNL AUTH 2 S.YOKOYAMA JRNL TITL SOLUTION STRUCTURE OF THE N-TERMINAL RNA BINDING DOMAIN IN JRNL TITL 2 DAZ-ASSOCIATED PROTEIN 1 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 REMARK 3 AUTHORS : BRUKER (XWINNMR), GUNTERT,P (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2DH8 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-MAR-06. REMARK 100 THE DEPOSITION ID IS D_1000025416. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 100MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 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 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 SER A -4 -60.73 -95.77 REMARK 500 1 SER A 4 -60.73 -102.16 REMARK 500 1 ALA A 6 86.73 -64.12 REMARK 500 1 TRP A 19 -35.25 -37.15 REMARK 500 1 THR A 21 135.10 -39.42 REMARK 500 1 GLU A 35 101.28 -53.61 REMARK 500 1 SER A 50 99.64 -49.49 REMARK 500 1 PRO A 72 -177.85 -69.81 REMARK 500 1 THR A 74 105.01 -160.46 REMARK 500 1 PRO A 84 2.56 -69.78 REMARK 500 1 ARG A 88 165.43 -44.35 REMARK 500 1 SER A 96 100.54 -39.45 REMARK 500 2 SER A -5 42.81 -104.74 REMARK 500 2 SER A -1 107.55 -160.88 REMARK 500 2 ASN A 3 119.70 -163.08 REMARK 500 2 ASP A 7 -62.30 -129.67 REMARK 500 2 THR A 21 134.90 -39.86 REMARK 500 2 GLU A 35 99.22 -54.41 REMARK 500 2 SER A 50 97.39 -51.69 REMARK 500 2 PRO A 61 2.60 -69.82 REMARK 500 2 ARG A 71 155.53 -49.85 REMARK 500 2 PRO A 72 -177.86 -69.80 REMARK 500 2 THR A 74 106.06 -162.62 REMARK 500 2 SER A 93 137.50 -34.63 REMARK 500 3 SER A -2 42.15 -95.47 REMARK 500 3 ALA A 6 43.72 -99.80 REMARK 500 3 GLU A 8 35.73 -93.83 REMARK 500 3 THR A 21 140.78 -34.85 REMARK 500 3 GLU A 35 100.91 -52.38 REMARK 500 3 THR A 46 -70.90 -119.01 REMARK 500 3 SER A 50 99.53 -40.52 REMARK 500 3 PRO A 61 2.22 -69.79 REMARK 500 3 ARG A 71 153.51 -40.15 REMARK 500 3 PRO A 72 -176.48 -69.76 REMARK 500 3 PRO A 92 3.18 -69.72 REMARK 500 3 SER A 93 118.80 -33.30 REMARK 500 3 SER A 96 106.72 -171.69 REMARK 500 4 ASN A 3 176.67 -51.36 REMARK 500 4 LEU A 17 177.70 -50.54 REMARK 500 4 THR A 21 132.52 -34.91 REMARK 500 4 GLU A 35 99.67 -54.09 REMARK 500 4 SER A 50 97.60 -43.10 REMARK 500 4 PRO A 61 0.30 -69.71 REMARK 500 4 ARG A 71 154.53 -45.17 REMARK 500 4 PRO A 72 -177.34 -69.79 REMARK 500 4 THR A 74 109.46 -163.04 REMARK 500 5 SER A -4 42.12 -84.18 REMARK 500 5 SER A -2 -49.03 -134.52 REMARK 500 5 GLU A 8 37.20 -92.96 REMARK 500 5 THR A 21 140.02 -37.77 REMARK 500 REMARK 500 THIS ENTRY HAS 208 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HSI002012495.1 RELATED DB: TARGETDB DBREF 2DH8 A 1 92 UNP Q96EP5 DAZP1_HUMAN 1 92 SEQADV 2DH8 GLY A -6 UNP Q96EP5 CLONING ARTIFACT SEQADV 2DH8 SER A -5 UNP Q96EP5 CLONING ARTIFACT SEQADV 2DH8 SER A -4 UNP Q96EP5 CLONING ARTIFACT SEQADV 2DH8 GLY A -3 UNP Q96EP5 CLONING ARTIFACT SEQADV 2DH8 SER A -2 UNP Q96EP5 CLONING ARTIFACT SEQADV 2DH8 SER A -1 UNP Q96EP5 CLONING ARTIFACT SEQADV 2DH8 GLY A 0 UNP Q96EP5 CLONING ARTIFACT SEQADV 2DH8 SER A 93 UNP Q96EP5 CLONING ARTIFACT SEQADV 2DH8 GLY A 94 UNP Q96EP5 CLONING ARTIFACT SEQADV 2DH8 PRO A 95 UNP Q96EP5 CLONING ARTIFACT SEQADV 2DH8 SER A 96 UNP Q96EP5 CLONING ARTIFACT SEQADV 2DH8 SER A 97 UNP Q96EP5 CLONING ARTIFACT SEQADV 2DH8 GLY A 98 UNP Q96EP5 CLONING ARTIFACT SEQRES 1 A 105 GLY SER SER GLY SER SER GLY MET ASN ASN SER GLY ALA SEQRES 2 A 105 ASP GLU ILE GLY LYS LEU PHE VAL GLY GLY LEU ASP TRP SEQRES 3 A 105 SER THR THR GLN GLU THR LEU ARG SER TYR PHE SER GLN SEQRES 4 A 105 TYR GLY GLU VAL VAL ASP CYS VAL ILE MET LYS ASP LYS SEQRES 5 A 105 THR THR ASN GLN SER ARG GLY PHE GLY PHE VAL LYS PHE SEQRES 6 A 105 LYS ASP PRO ASN CYS VAL GLY THR VAL LEU ALA SER ARG SEQRES 7 A 105 PRO HIS THR LEU ASP GLY ARG ASN ILE ASP PRO LYS PRO SEQRES 8 A 105 CYS THR PRO ARG GLY MET GLN PRO SER GLY PRO SER SER SEQRES 9 A 105 GLY HELIX 1 1 THR A 22 GLN A 32 1 11 HELIX 2 2 ASN A 62 ARG A 71 1 10 SHEET 1 A 3 LYS A 11 LEU A 12 0 SHEET 2 A 3 SER A 50 PHE A 58 -1 O VAL A 56 N LEU A 12 SHEET 3 A 3 VAL A 36 LYS A 43 -1 N ASP A 38 O LYS A 57 SHEET 1 B 2 HIS A 73 LEU A 75 0 SHEET 2 B 2 ARG A 78 ILE A 80 -1 O ARG A 78 N LEU A 75 CISPEP 1 ARG A 71 PRO A 72 1 0.05 CISPEP 2 ARG A 71 PRO A 72 2 0.05 CISPEP 3 ARG A 71 PRO A 72 3 0.02 CISPEP 4 ARG A 71 PRO A 72 4 0.00 CISPEP 5 ARG A 71 PRO A 72 5 0.00 CISPEP 6 ARG A 71 PRO A 72 6 0.09 CISPEP 7 ARG A 71 PRO A 72 7 0.06 CISPEP 8 ARG A 71 PRO A 72 8 0.02 CISPEP 9 ARG A 71 PRO A 72 9 -0.06 CISPEP 10 ARG A 71 PRO A 72 10 -0.04 CISPEP 11 ARG A 71 PRO A 72 11 0.02 CISPEP 12 ARG A 71 PRO A 72 12 0.08 CISPEP 13 ARG A 71 PRO A 72 13 -0.01 CISPEP 14 ARG A 71 PRO A 72 14 0.03 CISPEP 15 ARG A 71 PRO A 72 15 -0.06 CISPEP 16 ARG A 71 PRO A 72 16 0.08 CISPEP 17 ARG A 71 PRO A 72 17 0.05 CISPEP 18 ARG A 71 PRO A 72 18 0.03 CISPEP 19 ARG A 71 PRO A 72 19 -0.07 CISPEP 20 ARG A 71 PRO A 72 20 0.00 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