PDB Short entry for 2DMY HEADER RNA BINDING PROTEIN 24-APR-06 2DMY TITLE SOLUTION STRUCTURE OF DSRM DOMAIN IN SPERMATID PERINUCLEAR RNA-BIND TITLE 2 PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPERMATID PERINUCLEAR RNA-BINDING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DSRM DOMAIN; COMPND 5 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: STRBP; SOURCE 6 EXPRESSION_SYSTEM: CELL FREE SYNTHESIS; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: P051128-11; SOURCE 9 OTHER_DETAILS: CELL FREE PROTEIN SYNTHESIS KEYWDS DSRM 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.KADIRVEL,F.HE,Y.MUTO,M.INOUE,T.KIGAWA,M.SHIROUZU,T.TERADA, AUTHOR 2 S.YOKOYAMA,RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 3 09-MAR-22 2DMY 1 REMARK SEQADV REVDAT 2 24-FEB-09 2DMY 1 VERSN REVDAT 1 24-OCT-06 2DMY 0 JRNL AUTH S.KADIRVEL,F.HE,Y.MUTO,M.INOUE,T.KIGAWA,M.SHIROUZU,T.TERADA, JRNL AUTH 2 S.YOKOYAMA JRNL TITL SOLUTION STRUCTURE OF DSRM DOMAIN IN SPERMATID PERINUCLEAR JRNL TITL 2 RNA-BIND PROTEIN 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 2DMY COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-APR-06. REMARK 100 THE DEPOSITION ID IS D_1000025604. 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 : 120MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.8MM U-15, 13C; 20MM PHOSPHATE REMARK 210 BUFFER NA; 100MM NACL; 1MM D-DTT; REMARK 210 0.02% NAN3, 90%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 20031121, NMRVIEW 5.0.4, REMARK 210 KUJIRA 0.965, 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 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 13 46.04 -106.27 REMARK 500 1 PRO A 42 -175.51 -69.78 REMARK 500 1 ILE A 91 142.23 -35.91 REMARK 500 2 ALA A 15 -175.68 -62.46 REMARK 500 2 ASP A 17 113.67 -172.92 REMARK 500 2 LEU A 18 -69.52 -130.03 REMARK 500 2 ALA A 21 -35.28 -34.12 REMARK 500 3 SER A 3 114.96 -163.51 REMARK 500 3 SER A 5 115.65 -172.14 REMARK 500 3 SER A 6 115.45 -169.47 REMARK 500 3 LEU A 18 -51.99 -122.50 REMARK 500 3 PRO A 42 -174.39 -69.78 REMARK 500 3 ALA A 89 45.14 -97.13 REMARK 500 4 LYS A 14 147.88 -39.72 REMARK 500 4 PRO A 42 -174.53 -69.75 REMARK 500 4 ALA A 89 39.46 -92.70 REMARK 500 4 ILE A 91 176.07 -49.45 REMARK 500 4 SER A 92 108.12 -55.16 REMARK 500 4 PRO A 94 -173.85 -69.76 REMARK 500 4 SER A 95 122.82 -34.56 REMARK 500 5 LYS A 9 144.94 -173.90 REMARK 500 5 SER A 13 79.83 -113.85 REMARK 500 5 LYS A 14 42.52 -94.53 REMARK 500 5 ALA A 89 105.28 -174.85 REMARK 500 6 ILE A 10 58.53 -116.06 REMARK 500 6 ASP A 12 113.51 -168.80 REMARK 500 6 LYS A 14 96.55 -42.23 REMARK 500 6 ALA A 15 115.81 -169.19 REMARK 500 6 ASP A 17 77.07 -65.80 REMARK 500 6 PRO A 42 -178.07 -69.78 REMARK 500 6 ILE A 91 -19.64 -49.52 REMARK 500 6 SER A 95 109.65 -43.64 REMARK 500 7 ALA A 21 -35.47 -34.20 REMARK 500 7 PRO A 42 -173.92 -69.76 REMARK 500 7 ASP A 90 109.18 -168.55 REMARK 500 7 SER A 92 126.74 -171.06 REMARK 500 8 ALA A 15 113.40 -173.25 REMARK 500 8 ILE A 16 119.80 -37.14 REMARK 500 8 ASP A 17 76.47 -59.72 REMARK 500 8 PRO A 42 -174.11 -69.77 REMARK 500 8 ALA A 89 67.23 -116.49 REMARK 500 8 ILE A 91 145.11 -35.93 REMARK 500 9 SER A 2 -50.56 -126.93 REMARK 500 9 ASP A 12 96.70 -62.53 REMARK 500 9 ILE A 16 118.24 -37.53 REMARK 500 9 ASP A 17 76.70 -59.55 REMARK 500 9 MET A 19 -19.88 -49.41 REMARK 500 9 PRO A 42 -173.13 -69.72 REMARK 500 9 ALA A 89 51.74 -116.53 REMARK 500 9 ASP A 90 106.87 -167.80 REMARK 500 REMARK 500 THIS ENTRY HAS 115 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: HSK003002567.1 RELATED DB: TARGETDB DBREF 2DMY A 8 91 UNP Q9H7V1 Q9H7V1_HUMAN 111 194 SEQADV 2DMY GLY A 1 UNP Q9H7V1 CLONING ARTIFACT SEQADV 2DMY SER A 2 UNP Q9H7V1 CLONING ARTIFACT SEQADV 2DMY SER A 3 UNP Q9H7V1 CLONING ARTIFACT SEQADV 2DMY GLY A 4 UNP Q9H7V1 CLONING ARTIFACT SEQADV 2DMY SER A 5 UNP Q9H7V1 CLONING ARTIFACT SEQADV 2DMY SER A 6 UNP Q9H7V1 CLONING ARTIFACT SEQADV 2DMY GLY A 7 UNP Q9H7V1 CLONING ARTIFACT SEQADV 2DMY SER A 92 UNP Q9H7V1 CLONING ARTIFACT SEQADV 2DMY GLY A 93 UNP Q9H7V1 CLONING ARTIFACT SEQADV 2DMY PRO A 94 UNP Q9H7V1 CLONING ARTIFACT SEQADV 2DMY SER A 95 UNP Q9H7V1 CLONING ARTIFACT SEQADV 2DMY SER A 96 UNP Q9H7V1 CLONING ARTIFACT SEQADV 2DMY GLY A 97 UNP Q9H7V1 CLONING ARTIFACT SEQRES 1 A 97 GLY SER SER GLY SER SER GLY ARG LYS ILE LEU ASP SER SEQRES 2 A 97 LYS ALA ILE ASP LEU MET ASN ALA LEU MET ARG LEU ASN SEQRES 3 A 97 GLN ILE ARG PRO GLY LEU GLN TYR LYS LEU LEU SER GLN SEQRES 4 A 97 SER GLY PRO VAL HIS ALA PRO VAL PHE THR MET SER VAL SEQRES 5 A 97 ASP VAL ASP GLY THR THR TYR GLU ALA SER GLY PRO SER SEQRES 6 A 97 LYS LYS THR ALA LYS LEU HIS VAL ALA VAL LYS VAL LEU SEQRES 7 A 97 GLN ALA MET GLY TYR PRO THR GLY PHE ASP ALA ASP ILE SEQRES 8 A 97 SER GLY PRO SER SER GLY HELIX 1 1 ASN A 20 ILE A 28 1 9 HELIX 2 2 LYS A 66 MET A 81 1 16 SHEET 1 A 3 LYS A 35 SER A 40 0 SHEET 2 A 3 VAL A 47 VAL A 54 -1 O VAL A 47 N SER A 40 SHEET 3 A 3 THR A 57 GLY A 63 -1 O THR A 57 N VAL A 54 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