PDB Short entry for 2D9P HEADER RNA BINDING PROTEIN 12-DEC-05 2D9P TITLE SOLUTION STRUCTURE OF RNA BINDING DOMAIN 4 IN POLYADENYLATION BINDING TITLE 2 PROTEIN 3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLYADENYLATE-BINDING PROTEIN 3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RNA RECOGNITION MOTIF; COMPND 5 SYNONYM: POLYA, -BINDING PROTEIN 3, PABP 3, TESTIS-SPECIFIC POLYA, - COMPND 6 BINDING PROTEIN; COMPND 7 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: PABP3; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: P050516-01; SOURCE 8 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 K.TSUDA,Y.MUTO,M.INOUE,T.KIGAWA,T.TERADA,M.SHIROUZU,S.YOKOYAMA,RIKEN AUTHOR 2 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 3 09-MAR-22 2D9P 1 REMARK SEQADV REVDAT 2 24-FEB-09 2D9P 1 VERSN REVDAT 1 12-JUN-06 2D9P 0 JRNL AUTH K.TSUDA,Y.MUTO,M.INOUE,T.KIGAWA,T.TERADA,M.SHIROUZU, JRNL AUTH 2 S.YOKOYAMA JRNL TITL SOLUTION STRUCTURE OF RNA BINDING DOMAIN 4 IN JRNL TITL 2 POLYADENYLATION BINDING PROTEIN 3 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 2D9P COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-DEC-05. REMARK 100 THE DEPOSITION ID IS D_1000025160. 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 0.9321, 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 ARG A 287 38.15 35.49 REMARK 500 1 GLN A 292 95.71 -59.83 REMARK 500 1 PRO A 316 -17.34 -47.97 REMARK 500 1 GLU A 328 34.31 -94.67 REMARK 500 1 PHE A 335 147.54 -171.32 REMARK 500 1 GLU A 352 -19.19 -49.94 REMARK 500 1 ASN A 354 111.01 -36.30 REMARK 500 1 ALA A 359 -73.09 -116.43 REMARK 500 1 THR A 360 -47.62 -132.98 REMARK 500 1 TYR A 364 96.82 -68.43 REMARK 500 1 SER A 379 91.44 -60.95 REMARK 500 2 ASN A 300 37.87 74.50 REMARK 500 2 LEU A 310 -71.12 -67.61 REMARK 500 2 PRO A 316 -17.04 -48.02 REMARK 500 2 MET A 326 95.58 -68.39 REMARK 500 2 GLU A 352 -27.90 -39.99 REMARK 500 2 VAL A 358 -40.90 -131.95 REMARK 500 2 ALA A 359 -66.82 -130.21 REMARK 500 2 THR A 360 -54.52 -133.00 REMARK 500 2 LYS A 371 116.70 -161.86 REMARK 500 2 PRO A 378 150.37 -45.60 REMARK 500 3 ARG A 309 -36.49 -35.19 REMARK 500 3 LEU A 310 -75.12 -68.05 REMARK 500 3 PHE A 314 -30.41 -130.22 REMARK 500 3 PRO A 316 -17.59 -47.95 REMARK 500 3 ASN A 354 111.96 -34.25 REMARK 500 3 THR A 360 -53.23 -131.60 REMARK 500 3 LYS A 371 105.04 -170.25 REMARK 500 4 ASP A 302 157.93 -44.79 REMARK 500 4 LEU A 310 -74.50 -55.42 REMARK 500 4 PRO A 316 -17.88 -48.03 REMARK 500 4 PHE A 317 -61.09 -100.45 REMARK 500 4 ASN A 354 115.95 -34.02 REMARK 500 4 ALA A 359 -72.83 -118.55 REMARK 500 4 THR A 360 -51.74 -132.14 REMARK 500 4 GLN A 369 78.72 -101.06 REMARK 500 4 LYS A 371 -70.84 -106.73 REMARK 500 5 SER A 280 44.01 35.61 REMARK 500 5 LEU A 310 -70.53 -57.28 REMARK 500 5 PRO A 316 -17.10 -47.92 REMARK 500 5 ASN A 354 110.18 -34.89 REMARK 500 5 ALA A 359 -70.63 -125.11 REMARK 500 5 THR A 360 -52.91 -132.03 REMARK 500 5 ALA A 368 -61.41 -105.18 REMARK 500 5 GLU A 373 153.59 -44.99 REMARK 500 5 PRO A 378 156.48 -46.17 REMARK 500 6 SER A 283 147.26 -173.06 REMARK 500 6 LEU A 310 -70.29 -60.22 REMARK 500 6 PRO A 316 -17.02 -48.07 REMARK 500 6 GLU A 328 64.50 -113.37 REMARK 500 REMARK 500 THIS ENTRY HAS 177 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HSI002012034.1 RELATED DB: TARGETDB DBREF 2D9P A 286 375 UNP Q9H361 PABP3_HUMAN 286 375 SEQADV 2D9P GLY A 279 UNP Q9H361 CLONING ARTIFACT SEQADV 2D9P SER A 280 UNP Q9H361 CLONING ARTIFACT SEQADV 2D9P SER A 281 UNP Q9H361 CLONING ARTIFACT SEQADV 2D9P GLY A 282 UNP Q9H361 CLONING ARTIFACT SEQADV 2D9P SER A 283 UNP Q9H361 CLONING ARTIFACT SEQADV 2D9P SER A 284 UNP Q9H361 CLONING ARTIFACT SEQADV 2D9P GLY A 285 UNP Q9H361 CLONING ARTIFACT SEQADV 2D9P SER A 376 UNP Q9H361 CLONING ARTIFACT SEQADV 2D9P GLY A 377 UNP Q9H361 CLONING ARTIFACT SEQADV 2D9P PRO A 378 UNP Q9H361 CLONING ARTIFACT SEQADV 2D9P SER A 379 UNP Q9H361 CLONING ARTIFACT SEQADV 2D9P SER A 380 UNP Q9H361 CLONING ARTIFACT SEQADV 2D9P GLY A 381 UNP Q9H361 CLONING ARTIFACT SEQRES 1 A 103 GLY SER SER GLY SER SER GLY ASP ARG ILE THR ARG TYR SEQRES 2 A 103 GLN VAL VAL ASN LEU TYR VAL LYS ASN LEU ASP ASP GLY SEQRES 3 A 103 ILE ASP ASP GLU ARG LEU ARG LYS ALA PHE SER PRO PHE SEQRES 4 A 103 GLY THR ILE THR SER ALA LYS VAL MET MET GLU GLY GLY SEQRES 5 A 103 ARG SER LYS GLY PHE GLY PHE VAL CYS PHE SER SER PRO SEQRES 6 A 103 GLU GLU ALA THR LYS ALA VAL THR GLU MET ASN GLY ARG SEQRES 7 A 103 ILE VAL ALA THR LYS PRO LEU TYR VAL ALA LEU ALA GLN SEQRES 8 A 103 ARG LYS GLU GLU ARG GLN SER GLY PRO SER SER GLY HELIX 1 1 ASP A 306 ALA A 313 1 8 HELIX 2 2 SER A 342 ASN A 354 1 13 SHEET 1 A 4 ILE A 320 MET A 327 0 SHEET 2 A 4 SER A 332 PHE A 340 -1 O PHE A 337 N LYS A 324 SHEET 3 A 4 LEU A 296 LYS A 299 -1 N LEU A 296 O VAL A 338 SHEET 4 A 4 TYR A 364 LEU A 367 -1 O ALA A 366 N TYR A 297 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