HEADER RNA BINDING PROTEIN 28-JUN-07 2JRS TITLE SOLUTION NMR STRUCTURE OF CAPER RRM2 DOMAIN. NORTHEAST STRUCTURAL TITLE 2 GENOMICS TARGET HR4730A COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA-BINDING PROTEIN 39; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RRM2 DOMAIN: RESIDUES 235-331; COMPND 5 SYNONYM: RNA-BINDING MOTIF PROTEIN 39, RNA-BINDING REGION-CONTAINING COMPND 6 PROTEIN 2, HEPATOCELLULAR CARCINOMA PROTEIN 1, SPLICING FACTOR HCC1; 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: RBM39, HCC1, RNPC2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)+MAGIC; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: HR4730A-15.1; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET15 KEYWDS RNA BINDING MOTIF OF RBM39_HUMAN (CAPER), RRM2 DOMAIN, SOLUTION NMR KEYWDS 2 STRUCTURE, STRUCTURAL GENOMICS, PSI-2, PROTEIN STRUCTURE INITIATIVE, KEYWDS 3 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM, NESG, RNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR P.ROSSI,L.ZHAO,C.NWOSU,K.CUNNINGHAM,L.OWENS,R.XIAO,J.LIU,M.C.BARAN, AUTHOR 2 G.SWAPNA,T.B.ACTON,B.ROST,G.T.MONTELIONE,NORTHEAST STRUCTURAL AUTHOR 3 GENOMICS CONSORTIUM (NESG) REVDAT 4 19-FEB-20 2JRS 1 REMARK SEQADV REVDAT 3 24-FEB-09 2JRS 1 VERSN REVDAT 2 06-MAY-08 2JRS 1 SOURCE REVDAT 1 04-SEP-07 2JRS 0 JRNL AUTH P.ROSSI,R.XIAO,T.B.ACTON,G.T.MONTELIONE JRNL TITL SOLUTION NMR STRUCTURE OF CAPER RRM2 DOMAIN. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AUTOASSIGN 2.3.0, CNSSOLVE 1.1, X-PLOR NIH 2.11.2 REMARK 3 AUTHORS : ZIMMERMAN, MOSELEY, KULIKOWSKI AND MONTELIONE REMARK 3 (AUTOASSIGN), BRUNGER, ADAMS, CLORE, GROS, NILGES REMARK 3 AND READ (CNSSOLVE), SCHWIETERS, KUSZEWSKI, REMARK 3 TJANDRA AND CLORE (X-PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2JRS COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-JUL-07. REMARK 100 THE DEPOSITION ID IS D_1000100208. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 0.1 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.3 MM [U-100% 13C; U-100% 15N] REMARK 210 PROTEIN, 0.02 % SODIUM AZIDE, 20 REMARK 210 MM MES, 100 MM SODIUM CHLORIDE, REMARK 210 5 MM CALCIUM CHLORIDE, 10 MM DTT, REMARK 210 95% H2O/5% D2O; 1.1 MM [U-5% REMARK 210 13C; U-100% 15N] PROTEIN, 0.02 % REMARK 210 SODIUM AZIDE, 20 MM MES, 100 MM REMARK 210 SODIUM CHLORIDE, 5 MM CALCIUM REMARK 210 CHLORIDE, 10 MM DTT, 95% H2O/5% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-15N NOESY; 3D 1H-13C REMARK 210 NOESY; 2D 1H-13C HSQC; 2D 1H-15N REMARK 210 HSQC; 2D 1H-13C HSQC REMARK 210 STEREOSPECIFIC METHYL; HETNOE; REMARK 210 3D HNCACB; 3D HN(COCA)CB; 3D REMARK 210 HNCO; 3D HBHA(CO)NH; 3D HCCH- REMARK 210 TOCSY; 3D HCCH-COSY; 3D CCH-TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : AUTOSTRUCTURE 2.1.1, NMRPIPE REMARK 210 2.4, SPARKY 2.112, TOPSPIN 1.3, REMARK 210 DYANA, PSVS 1.3, PDBSTAT 5.0, REMARK 210 MOLMOL 2K.2, MOLPROBITY, REMARK 210 PROCHECKNMR REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: STRUCTURE DETERMINED BY TRIPLE RESONANCE NMR SPECTROSCOPY. REMARK 210 NOESY ASSIGNMENTS MADE WITH ITERATIVE METHOD USING CHEMICAL REMARK 210 SHIFTS (TALOS) FOR DIHEDRAL ANGLE INFERENCE, AND DYANA FOR REMARK 210 SIMULATED ANNEALING MD LOWEST TARGET FUNCTION SELECTED. REMARK 210 CONVERGED STRUCTURES ARE FURTHER REFINED USING NIH-XPLOR REMARK 210 FOLLOWED BY CNS IN EXPLICIT WATER SHELL (NIELGES PROTOCOL WITH REMARK 210 PARAM19). ASSIGNMENT STATS (EXCLUDING N-TERM TAG): BACKBONE REMARK 210 99.19%, SIDECHAIN 94.31%, AROMATIC (SC) 100%, VL METHYL REMARK 210 STEREOSPECIFIC 100%, UNAMBIGUOUS SIDECHAIN NH2 100%. STRUCTURE REMARK 210 BASED ON 1252 NOE, 44 H-BOND, 84 DIHEDRAL. 100 STRUCTURES REMARK 210 CALCULATED 20 LOWEST ENERGY SUBMITTED. MAX NOE VIOLATION 0.30 A REMARK 210 (1 MODEL), MAX DIHEDRAL VIOLATION 4.0 DEG. 5 CLOSE CONTACTS REMARK 210 TOTAL PER 20 MODELS. STRUCTURE QUALITY FACTOR PSVS 1.3: ORDERED REMARK 210 RESIDUES RANGES - ALPHA HELIX (40-47, 78-88), B-STRAND (53-61, REMARK 210 66-75, 27-32, 99-101) [S(PHI)+S(PSI)] > 1.8. RMSD 0.4 BB, 1.0 REMARK 210 ALL HEAVY ATOMS. RAMACHANDRAN: 85.4% MOST FAV, 12.4% ADDTL ALLOW, REMARK 210 2.3 GENEROUSLY ALLOW, 0.0% DISALLOW. PROCHECK (PSI-PHI): -0.46/- REMARK 210 1.49 (RAW/Z), PROCHECK (ALL): -0.24/-1.42 (RAW/Z), MOLPROBITY REMARK 210 CLASH: 15.06/-1.06 (RAW/Z). RPF SCORES ALL ASSIGNED RESIDUES REMARK 210 (FIT OF NOESY PEAKLISTS TO STRUCTURE): RECALL: 0.959, PRECISION: REMARK 210 0.935, F-MEASURE: 0.947, DP-SCORE: 0.775. 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 HIS A 3 88.88 61.09 REMARK 500 1 HIS A 6 110.21 -160.68 REMARK 500 1 SER A 9 98.52 -68.84 REMARK 500 1 HIS A 10 96.05 -56.02 REMARK 500 1 MET A 11 179.68 69.64 REMARK 500 1 ALA A 12 -52.44 73.00 REMARK 500 1 GLN A 20 90.25 57.68 REMARK 500 1 SER A 23 -166.64 68.77 REMARK 500 1 ALA A 24 -11.57 72.40 REMARK 500 1 SER A 33 11.20 -163.96 REMARK 500 1 ASN A 37 -8.81 -143.30 REMARK 500 1 ASP A 61 88.45 -66.61 REMARK 500 1 ALA A 94 45.36 -98.53 REMARK 500 1 HIS A 102 46.64 -82.00 REMARK 500 1 VAL A 103 -78.60 56.69 REMARK 500 1 GLU A 105 -50.47 -142.65 REMARK 500 2 HIS A 3 161.88 63.54 REMARK 500 2 HIS A 4 36.45 -141.30 REMARK 500 2 HIS A 7 130.98 55.00 REMARK 500 2 ALA A 13 124.14 66.81 REMARK 500 2 ALA A 14 16.67 -149.09 REMARK 500 2 ALA A 16 78.46 61.20 REMARK 500 2 ASN A 18 44.73 -79.86 REMARK 500 2 PRO A 26 101.77 -57.64 REMARK 500 2 SER A 33 24.98 -164.42 REMARK 500 2 HIS A 35 48.65 -108.83 REMARK 500 2 ASN A 37 37.06 -142.50 REMARK 500 2 SER A 62 17.43 59.28 REMARK 500 2 ALA A 94 16.90 59.49 REMARK 500 3 HIS A 4 118.23 -165.01 REMARK 500 3 HIS A 10 -41.93 72.12 REMARK 500 3 ALA A 12 74.90 -106.74 REMARK 500 3 ALA A 13 -70.64 64.25 REMARK 500 3 ALA A 16 99.86 67.17 REMARK 500 3 ASN A 18 138.89 66.61 REMARK 500 3 ALA A 24 -35.31 73.34 REMARK 500 3 SER A 33 15.46 -174.72 REMARK 500 3 PHE A 36 9.73 55.37 REMARK 500 3 ARG A 66 -163.90 -112.99 REMARK 500 3 ASN A 89 85.90 -68.54 REMARK 500 3 ALA A 94 18.67 59.15 REMARK 500 3 GLU A 105 -40.87 74.82 REMARK 500 4 HIS A 3 121.25 66.95 REMARK 500 4 HIS A 4 85.99 -68.14 REMARK 500 4 HIS A 6 -179.18 -67.44 REMARK 500 4 HIS A 7 -75.52 -69.95 REMARK 500 4 HIS A 8 142.64 62.96 REMARK 500 4 SER A 9 170.84 67.19 REMARK 500 4 HIS A 10 76.42 -154.61 REMARK 500 4 MET A 15 104.97 -55.65 REMARK 500 REMARK 500 THIS ENTRY HAS 304 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HR4730A RELATED DB: TARGETDB REMARK 900 RELATED ID: 15343 RELATED DB: BMRB DBREF 2JRS A 12 108 UNP Q14498 RBM39_HUMAN 235 331 SEQADV 2JRS MET A 1 UNP Q14498 EXPRESSION TAG SEQADV 2JRS GLY A 2 UNP Q14498 EXPRESSION TAG SEQADV 2JRS HIS A 3 UNP Q14498 EXPRESSION TAG SEQADV 2JRS HIS A 4 UNP Q14498 EXPRESSION TAG SEQADV 2JRS HIS A 5 UNP Q14498 EXPRESSION TAG SEQADV 2JRS HIS A 6 UNP Q14498 EXPRESSION TAG SEQADV 2JRS HIS A 7 UNP Q14498 EXPRESSION TAG SEQADV 2JRS HIS A 8 UNP Q14498 EXPRESSION TAG SEQADV 2JRS SER A 9 UNP Q14498 EXPRESSION TAG SEQADV 2JRS HIS A 10 UNP Q14498 EXPRESSION TAG SEQADV 2JRS MET A 11 UNP Q14498 EXPRESSION TAG SEQRES 1 A 108 MET GLY HIS HIS HIS HIS HIS HIS SER HIS MET ALA ALA SEQRES 2 A 108 ALA MET ALA ASN ASN LEU GLN LYS GLY SER ALA GLY PRO SEQRES 3 A 108 MET ARG LEU TYR VAL GLY SER LEU HIS PHE ASN ILE THR SEQRES 4 A 108 GLU ASP MET LEU ARG GLY ILE PHE GLU PRO PHE GLY ARG SEQRES 5 A 108 ILE GLU SER ILE GLN LEU MET MET ASP SER GLU THR GLY SEQRES 6 A 108 ARG SER LYS GLY TYR GLY PHE ILE THR PHE SER ASP SER SEQRES 7 A 108 GLU CYS ALA LYS LYS ALA LEU GLU GLN LEU ASN GLY PHE SEQRES 8 A 108 GLU LEU ALA GLY ARG PRO MET LYS VAL GLY HIS VAL THR SEQRES 9 A 108 GLU ARG THR ASP HELIX 1 1 THR A 39 GLU A 48 1 10 HELIX 2 2 ASP A 77 ASN A 89 1 13 SHEET 1 A 4 ILE A 53 MET A 60 0 SHEET 2 A 4 SER A 67 PHE A 75 -1 O PHE A 72 N GLN A 57 SHEET 3 A 4 MET A 27 GLY A 32 -1 N MET A 27 O PHE A 75 SHEET 4 A 4 LYS A 99 GLY A 101 -1 O GLY A 101 N TYR A 30 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 MODEL 1