PDB Short entry for 2EPD HEADER PROTEIN BINDING 29-MAR-07 2EPD TITLE SOLUTION STRUCTURE OF SH3 DOMAIN IN RHO-GTPASE-ACTIVATING PROTEIN 4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RHO GTPASE-ACTIVATING PROTEIN 4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SH3 DOMAIN; COMPND 5 SYNONYM: RHO-GAP HEMATOPOIETIC PROTEIN C1, P115; COMPND 6 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: ARHGAP4, KIAA0131, RGC1, RHOGAP4; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: P060130-05; SOURCE 8 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS KEYWDS SH3 DOMAIN, STRUCTURAL GENOMICS, NPPSFA, NATIONAL PROJECT ON PROTEIN KEYWDS 2 STRUCTURAL AND FUNCTIONAL ANALYSES, RIKEN STRUCTURAL KEYWDS 3 GENOMICS/PROTEOMICS INITIATIVE, RSGI, PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR W.TANABE,K.TSUDA,Y.MUTO,M.INOUE,T.KIGAWA,T.TERADA,M.SHIROUZU, AUTHOR 2 S.YOKOYAMA,RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 3 09-MAR-22 2EPD 1 REMARK SEQADV REVDAT 2 24-FEB-09 2EPD 1 VERSN REVDAT 1 02-OCT-07 2EPD 0 JRNL AUTH W.TANABE,K.TSUDA,Y.MUTO,M.INOUE,T.KIGAWA,T.TERADA, JRNL AUTH 2 M.SHIROUZU,S.YOKOYAMA JRNL TITL SOLUTION STRUCTURE OF SH3 DOMAIN IN RHO-GTPASE-ACTIVATING JRNL TITL 2 PROTEIN 4 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 2EPD COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-JUN-07. REMARK 100 THE DEPOSITION ID IS D_1000026942. 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 : 1.14MM 13C-15N PROTEIN, 20MM D REMARK 210 -TRIS-HCL (PH7.0), 100MM NACL, REMARK 210 1MM D-DTT, 0.02% NAN3, 0.05MM REMARK 210 ZNCL2, 1MM IDA; 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 20060702, NMRVIEW 5.0.4, REMARK 210 KUJIRA 0.9820, 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 : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS, STRUCTURES REMARK 210 WITH THE LOWEST ENERGY, TARGET REMARK 210 FUNCTION 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 740 43.02 70.95 REMARK 500 1 ARG A 769 129.78 -35.14 REMARK 500 1 ARG A 778 141.94 -38.99 REMARK 500 1 ASN A 789 99.33 -57.92 REMARK 500 1 ALA A 804 109.78 -47.90 REMARK 500 1 THR A 806 171.02 -45.67 REMARK 500 1 ALA A 813 116.82 -168.00 REMARK 500 2 SER A 744 44.10 -108.16 REMARK 500 2 ASN A 789 71.35 -68.92 REMARK 500 2 ALA A 813 119.93 -34.52 REMARK 500 3 GLU A 746 40.43 -106.06 REMARK 500 3 ASN A 789 72.14 -66.80 REMARK 500 3 VAL A 811 -31.41 -37.79 REMARK 500 4 SER A 741 116.72 -36.90 REMARK 500 4 ARG A 769 134.14 -39.43 REMARK 500 4 ASN A 789 76.33 -66.93 REMARK 500 4 VAL A 810 105.58 -53.59 REMARK 500 5 GLU A 746 157.83 -48.19 REMARK 500 5 ASN A 789 98.68 -57.88 REMARK 500 5 ALA A 804 -37.23 -35.72 REMARK 500 6 SER A 743 42.36 -89.20 REMARK 500 6 ARG A 769 128.21 -37.37 REMARK 500 6 ASN A 789 73.38 -67.13 REMARK 500 6 TYR A 799 42.72 -90.72 REMARK 500 6 ALA A 804 137.38 -34.82 REMARK 500 7 SER A 743 42.15 -98.25 REMARK 500 7 GLU A 746 162.40 -41.73 REMARK 500 7 ASN A 789 92.50 -52.92 REMARK 500 7 ALA A 804 119.77 -35.90 REMARK 500 7 THR A 806 40.62 -96.73 REMARK 500 8 GLU A 746 37.57 -88.47 REMARK 500 8 ARG A 769 124.85 -35.16 REMARK 500 8 ASN A 789 95.85 -55.30 REMARK 500 9 ARG A 769 127.66 -39.71 REMARK 500 9 ASN A 789 73.64 -66.93 REMARK 500 9 TYR A 799 37.21 -90.31 REMARK 500 9 ALA A 804 95.47 -63.82 REMARK 500 9 THR A 806 45.61 -78.25 REMARK 500 9 GLU A 807 42.85 35.69 REMARK 500 9 VAL A 810 153.94 -48.89 REMARK 500 10 ARG A 769 126.58 -34.32 REMARK 500 10 ASN A 789 93.93 -53.48 REMARK 500 10 TYR A 799 32.53 -92.08 REMARK 500 10 ALA A 804 143.15 -37.43 REMARK 500 10 VAL A 811 39.60 -88.71 REMARK 500 11 SER A 744 42.36 -98.96 REMARK 500 11 ASN A 789 98.43 -57.57 REMARK 500 11 THR A 806 96.76 -62.37 REMARK 500 11 LYS A 808 40.62 -101.11 REMARK 500 12 ASN A 789 93.75 -52.38 REMARK 500 REMARK 500 THIS ENTRY HAS 86 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF 2EPD A 746 814 UNP P98171 RHG04_HUMAN 746 814 SEQADV 2EPD GLY A 739 UNP P98171 EXPRESSION TAG SEQADV 2EPD SER A 740 UNP P98171 EXPRESSION TAG SEQADV 2EPD SER A 741 UNP P98171 EXPRESSION TAG SEQADV 2EPD GLY A 742 UNP P98171 EXPRESSION TAG SEQADV 2EPD SER A 743 UNP P98171 EXPRESSION TAG SEQADV 2EPD SER A 744 UNP P98171 EXPRESSION TAG SEQADV 2EPD GLY A 745 UNP P98171 EXPRESSION TAG SEQRES 1 A 76 GLY SER SER GLY SER SER GLY GLU GLY VAL VAL GLU ALA SEQRES 2 A 76 VAL ALA CYS PHE ALA TYR THR GLY ARG THR ALA GLN GLU SEQRES 3 A 76 LEU SER PHE ARG ARG GLY ASP VAL LEU ARG LEU HIS GLU SEQRES 4 A 76 ARG ALA SER SER ASP TRP TRP ARG GLY GLU HIS ASN GLY SEQRES 5 A 76 MET ARG GLY LEU ILE PRO HIS LYS TYR ILE THR LEU PRO SEQRES 6 A 76 ALA GLY THR GLU LYS GLN VAL VAL GLY ALA GLY SHEET 1 A 5 MET A 791 PRO A 796 0 SHEET 2 A 5 TRP A 783 HIS A 788 -1 N GLY A 786 O GLY A 793 SHEET 3 A 5 VAL A 772 SER A 780 -1 N HIS A 776 O ARG A 785 SHEET 4 A 5 VAL A 749 ALA A 753 -1 N VAL A 749 O LEU A 775 SHEET 5 A 5 ILE A 800 THR A 801 -1 O THR A 801 N VAL A 752 SHEET 1 B 2 TYR A 757 THR A 758 0 SHEET 2 B 2 SER A 766 PHE A 767 -1 O PHE A 767 N TYR A 757 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