HEADER RNA BINDING PROTEIN 18-MAY-99 1HD0 TITLE HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN D0 (HNRNP D0 RBD1), NMR COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN D0); COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RNA-BINDING 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 CELL: HELA; SOURCE 6 CELLULAR_LOCATION: NUCLEUS; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_CELL: BL21(DE3); SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET3A; SOURCE 12 EXPRESSION_SYSTEM_GENE: PET3A; SOURCE 13 OTHER_DETAILS: PCR KEYWDS RNA-BINDING DOMAIN, RNA BINDING PROTEIN EXPDTA SOLUTION NMR AUTHOR T.NAGATA,Y.KURIHARA,G.MATSUDA,J.SAEKI,T.KOHNO,Y.YANAGIDA,F.ISHIKAWA, AUTHOR 2 S.UESUGI,M.KATAHIRA REVDAT 4 27-DEC-23 1HD0 1 REMARK REVDAT 3 23-FEB-22 1HD0 1 REMARK REVDAT 2 24-FEB-09 1HD0 1 VERSN REVDAT 1 18-MAY-00 1HD0 0 JRNL AUTH T.NAGATA,Y.KURIHARA,G.MATSUDA,J.SAEKI,T.KOHNO,Y.YANAGIDA, JRNL AUTH 2 F.ISHIKAWA,S.UESUGI,M.KATAHIRA JRNL TITL STRUCTURE AND INTERACTIONS WITH RNA OF THE N-TERMINAL JRNL TITL 2 UUAG-SPECIFIC RNA-BINDING DOMAIN OF HNRNP D0. JRNL REF J.MOL.BIOL. V. 287 221 1999 JRNL REFN ISSN 0022-2836 JRNL PMID 10080887 JRNL DOI 10.1006/JMBI.1999.2616 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1, X-PLOR 3.8 REMARK 3 AUTHORS : BRUNGER (X-PLOR), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1HD0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-MAY-99. REMARK 100 THE DEPOSITION ID IS D_1000001080. 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 MM REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; TOCSY; DQF-COSY; 1H-15N REMARK 210 2D HSQC; 15N-EDITED NOESY-HSQC; REMARK 210 13C-EDITED NOESY-HSQC; 15N- REMARK 210 EDITED TOCSY-HSQC; HNCA; HNCO; REMARK 210 HN(CO)CA; HNCACB; CBCA(CO)NH; REMARK 210 HNHA; HCCH-COSY; HCCH-TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AMX500; DRX600 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR 3.1, X-PLOR 3.8 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWER ENERGIES REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: RESTRAINED ENERGY MINIMIZED MEAN STRUCTURE. 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 H PHE A 100 H ALA A 172 0.91 REMARK 500 HD23 LEU A 128 HG LEU A 130 1.13 REMARK 500 O GLY A 102 H ASP A 168 1.14 REMARK 500 HD12 LEU A 128 HG LEU A 130 1.17 REMARK 500 HD22 LEU A 128 HD12 LEU A 130 1.19 REMARK 500 OE2 GLU A 147 H GLU A 149 1.20 REMARK 500 HB2 ASP A 131 HB2 ARG A 136 1.21 REMARK 500 HG21 VAL A 154 HE1 HIS A 160 1.24 REMARK 500 HG LEU A 128 HD12 LEU A 130 1.25 REMARK 500 O LEU A 130 HD3 PRO A 132 1.27 REMARK 500 HG LEU A 128 HD13 LEU A 130 1.28 REMARK 500 OE2 GLU A 147 HB2 GLU A 149 1.28 REMARK 500 HG11 VAL A 166 H ILE A 167 1.34 REMARK 500 HB2 LYS A 129 O PHE A 140 1.40 REMARK 500 CA MET A 99 HB1 ALA A 172 1.43 REMARK 500 O ASP A 115 H SER A 118 1.47 REMARK 500 O MET A 99 HB3 ALA A 172 1.48 REMARK 500 N MET A 99 HB1 ALA A 172 1.50 REMARK 500 HD22 LEU A 128 CD2 LEU A 130 1.52 REMARK 500 OD1 ASP A 112 H LEU A 113 1.52 REMARK 500 HD22 LEU A 128 CD1 LEU A 130 1.52 REMARK 500 OE2 GLU A 147 N GLU A 149 1.54 REMARK 500 HG LEU A 128 CD1 LEU A 130 1.54 REMARK 500 CD2 LEU A 128 HD12 LEU A 130 1.54 REMARK 500 C MET A 99 HB1 ALA A 172 1.56 REMARK 500 O ILE A 167 HD3 PRO A 169 1.58 REMARK 500 HD22 LEU A 128 CG LEU A 130 1.58 REMARK 500 O GLU A 147 HG SER A 150 1.59 REMARK 500 CB LYS A 129 O PHE A 140 1.79 REMARK 500 O GLU A 147 OG SER A 150 1.81 REMARK 500 CD2 LEU A 128 CG LEU A 130 1.85 REMARK 500 CG LEU A 128 CD1 LEU A 130 1.85 REMARK 500 C MET A 99 CB ALA A 172 1.90 REMARK 500 O LEU A 130 CD PRO A 132 1.91 REMARK 500 OE2 GLU A 147 CB GLU A 149 1.96 REMARK 500 O THR A 109 OD1 ASP A 112 1.96 REMARK 500 CD2 LEU A 128 CD1 LEU A 130 1.98 REMARK 500 O GLY A 102 N ASP A 168 2.02 REMARK 500 O GLU A 149 OD2 ASP A 152 2.05 REMARK 500 O LEU A 130 N PRO A 132 2.08 REMARK 500 CD2 LEU A 128 CD2 LEU A 130 2.12 REMARK 500 OE2 GLU A 147 CA GLU A 149 2.13 REMARK 500 O SER A 105 OG1 THR A 108 2.18 REMARK 500 O MET A 99 CB ALA A 172 2.19 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 TYR A 116 -33.79 -39.14 REMARK 500 ASP A 131 78.91 -39.35 REMARK 500 SER A 137 90.17 -63.83 REMARK 500 ARG A 138 33.48 -89.70 REMARK 500 PHE A 140 121.36 -170.38 REMARK 500 LYS A 161 72.93 -157.24 REMARK 500 ARG A 171 49.51 -90.09 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 136 0.15 SIDE CHAIN REMARK 500 ARG A 138 0.30 SIDE CHAIN REMARK 500 ARG A 171 0.29 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1HD1 RELATED DB: PDB DBREF 1HD0 A 98 172 UNP Q14103 HNRPD_HUMAN 98 172 SEQRES 1 A 75 LYS MET PHE ILE GLY GLY LEU SER TRP ASP THR THR LYS SEQRES 2 A 75 LYS ASP LEU LYS ASP TYR PHE SER LYS PHE GLY GLU VAL SEQRES 3 A 75 VAL ASP CYS THR LEU LYS LEU ASP PRO ILE THR GLY ARG SEQRES 4 A 75 SER ARG GLY PHE GLY PHE VAL LEU PHE LYS GLU SER GLU SEQRES 5 A 75 SER VAL ASP LYS VAL MET ASP GLN LYS GLU HIS LYS LEU SEQRES 6 A 75 ASN GLY LYS VAL ILE ASP PRO LYS ARG ALA HELIX 1 H1 LYS A 110 PHE A 120 5 11 HELIX 2 H2 SER A 148 GLN A 157 5 10 SHEET 1 S1 1 LYS A 98 GLY A 102 0 SHEET 1 S2 1 VAL A 123 LYS A 129 0 SHEET 1 S3 1 PHE A 140 PHE A 145 0 SHEET 1 S4 1 ASP A 168 ARG A 171 0 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