PDB Short entry for 2DNZ HEADER RNA BINDING PROTEIN 27-APR-06 2DNZ TITLE SOLUTION STRUCTURE OF THE SECOND RNA BINDING DOMAIN OF RNA BINDING TITLE 2 MOTIF PROTEIN 23 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE RNA-BINDING PROTEIN 23; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RNA RECOGNITION MOTIF; COMPND 5 SYNONYM: RNA-BINDING MOTIF PROTEIN 23, RNA- BINDING REGION-CONTAINING COMPND 6 PROTEIN 4, SPLICING FACTOR SF2; 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: RBM23; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: P050516-02; SOURCE 8 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS KEYWDS RNA RECOGNITION MOTIF, RRM, RNA BINDING DOMAIN, RBD, RNP, STRUCTURAL KEYWDS 2 GENOMICS, NPPSFA, NATIONAL PROJECT ON PROTEIN STRUCTURAL AND KEYWDS 3 FUNCTIONAL ANALYSES, RIKEN STRUCTURAL GENOMICS/PROTEOMICS KEYWDS 4 INITIATIVE, RSGI, RNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR S.SUZUKI,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 2DNZ 1 REMARK SEQADV REVDAT 2 24-FEB-09 2DNZ 1 VERSN REVDAT 1 17-APR-07 2DNZ 0 JRNL AUTH S.SUZUKI,Y.MUTO,M.INOUE,T.KIGAWA,T.TERADA,M.SHIROUZU, JRNL AUTH 2 S.YOKOYAMA JRNL TITL SOLUTION STRUCTURE OF THE SECOND RNA BINDING DOMAIN OF RNA JRNL TITL 2 BINDING MOTIF PROTEIN 23 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 2DNZ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-MAY-06. REMARK 100 THE DEPOSITION ID IS D_1000025637. 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 : 1.15MM 13C/15N-PROTEIN; 20MM D REMARK 210 -TRIS-HCL(PH7.0); 100MM NACL; REMARK 210 1MM D-DTT; 0.02% NAN3; 90% H2O, REMARK 210 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 0.9321, OLIVIA 1.10.5, REMARK 210 CYANA 2.0.17 REMARK 210 METHOD USED : TORSION ANGLE DYANAMICS, REMARK 210 SIMULATED ANNEALING 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: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR REMARK 210 SPECTROSCOPY. 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 228 120.30 -37.13 REMARK 500 1 SER A 235 44.67 72.82 REMARK 500 1 ILE A 240 152.20 -44.66 REMARK 500 1 PRO A 251 2.88 -69.81 REMARK 500 1 SER A 269 103.78 -38.18 REMARK 500 2 SER A 229 33.48 -92.20 REMARK 500 2 SER A 235 47.24 74.12 REMARK 500 2 ILE A 240 154.47 -40.07 REMARK 500 2 PRO A 251 3.02 -69.79 REMARK 500 2 SER A 269 103.32 -35.34 REMARK 500 2 LEU A 295 -62.12 -98.17 REMARK 500 2 SER A 317 99.93 -69.15 REMARK 500 3 SER A 235 43.67 72.71 REMARK 500 3 ILE A 240 147.90 -38.64 REMARK 500 3 PRO A 251 2.42 -69.70 REMARK 500 3 ASP A 263 -179.40 -58.04 REMARK 500 3 SER A 269 118.63 -34.94 REMARK 500 3 ASN A 291 108.78 -46.03 REMARK 500 3 GLU A 307 78.50 -105.82 REMARK 500 4 SER A 229 91.53 -65.43 REMARK 500 4 SER A 235 44.20 71.98 REMARK 500 4 PRO A 251 2.92 -69.79 REMARK 500 4 ASP A 263 -179.26 -68.36 REMARK 500 4 ASN A 291 98.16 -45.15 REMARK 500 4 ALA A 296 45.09 -105.02 REMARK 500 4 SER A 316 52.34 72.33 REMARK 500 5 SER A 235 45.71 71.32 REMARK 500 5 PRO A 251 2.52 -69.76 REMARK 500 5 SER A 269 106.77 -38.59 REMARK 500 5 ASN A 291 103.44 -55.09 REMARK 500 5 GLU A 294 99.31 -56.70 REMARK 500 5 SER A 317 42.53 34.55 REMARK 500 6 SER A 235 45.61 72.29 REMARK 500 6 PRO A 251 2.93 -69.82 REMARK 500 6 ASP A 263 -178.07 -62.46 REMARK 500 6 SER A 269 110.15 -34.98 REMARK 500 6 ALA A 296 41.02 -105.70 REMARK 500 6 THR A 306 97.16 -66.91 REMARK 500 6 SER A 313 123.66 -36.84 REMARK 500 6 PRO A 315 2.46 -69.78 REMARK 500 6 SER A 316 144.27 -34.58 REMARK 500 7 PRO A 251 2.27 -69.77 REMARK 500 7 SER A 269 106.67 -34.94 REMARK 500 7 ASN A 291 105.76 -43.52 REMARK 500 7 VAL A 305 125.06 -39.30 REMARK 500 8 SER A 235 43.20 73.05 REMARK 500 8 ILE A 240 150.75 -35.38 REMARK 500 8 PRO A 251 3.46 -69.70 REMARK 500 8 SER A 269 94.33 -39.21 REMARK 500 8 ASN A 291 103.41 -46.20 REMARK 500 REMARK 500 THIS ENTRY HAS 132 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR DETERMINED REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: AUTHOR DETERMINED DBREF 2DNZ A 231 312 UNP Q86U06 RBM23_HUMAN 231 312 SEQADV 2DNZ GLY A 224 UNP Q86U06 CLONING ARTIFACT SEQADV 2DNZ SER A 225 UNP Q86U06 CLONING ARTIFACT SEQADV 2DNZ SER A 226 UNP Q86U06 CLONING ARTIFACT SEQADV 2DNZ GLY A 227 UNP Q86U06 CLONING ARTIFACT SEQADV 2DNZ SER A 228 UNP Q86U06 CLONING ARTIFACT SEQADV 2DNZ SER A 229 UNP Q86U06 CLONING ARTIFACT SEQADV 2DNZ GLY A 230 UNP Q86U06 CLONING ARTIFACT SEQADV 2DNZ SER A 313 UNP Q86U06 CLONING ARTIFACT SEQADV 2DNZ GLY A 314 UNP Q86U06 CLONING ARTIFACT SEQADV 2DNZ PRO A 315 UNP Q86U06 CLONING ARTIFACT SEQADV 2DNZ SER A 316 UNP Q86U06 CLONING ARTIFACT SEQADV 2DNZ SER A 317 UNP Q86U06 CLONING ARTIFACT SEQADV 2DNZ GLY A 318 UNP Q86U06 CLONING ARTIFACT SEQRES 1 A 95 GLY SER SER GLY SER SER GLY LEU TYR VAL GLY SER LEU SEQRES 2 A 95 HIS PHE ASN ILE THR GLU ASP MET LEU ARG GLY ILE PHE SEQRES 3 A 95 GLU PRO PHE GLY LYS ILE ASP ASN ILE VAL LEU MET LYS SEQRES 4 A 95 ASP SER ASP THR GLY ARG SER LYS GLY TYR GLY PHE ILE SEQRES 5 A 95 THR PHE SER ASP SER GLU CYS ALA ARG ARG ALA LEU GLU SEQRES 6 A 95 GLN LEU ASN GLY PHE GLU LEU ALA GLY ARG PRO MET ARG SEQRES 7 A 95 VAL GLY HIS VAL THR GLU ARG LEU ASP GLY GLY SER GLY SEQRES 8 A 95 PRO SER SER GLY HELIX 1 1 GLU A 242 PHE A 249 1 8 HELIX 2 2 SER A 280 LEU A 290 1 11 SHEET 1 A 4 ILE A 255 LEU A 260 0 SHEET 2 A 4 TYR A 272 PHE A 277 -1 O PHE A 274 N VAL A 259 SHEET 3 A 4 LEU A 231 GLY A 234 -1 N LEU A 231 O ILE A 275 SHEET 4 A 4 ARG A 301 HIS A 304 -1 O GLY A 303 N TYR A 232 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