PDB Short entry for 2DKY HEADER SIGNALING PROTEIN 14-APR-06 2DKY TITLE SOLUTION STRUCTURE OF THE SAM-DOMAIN OF RHO-GTPASE-ACTIVATING PROTEIN TITLE 2 7 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RHO-GTPASE-ACTIVATING PROTEIN 7; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SAM-DOMAIN; COMPND 5 SYNONYM: RHO-TYPE GTPASE-ACTIVATING PROTEIN 7, DELETED IN LIVER COMPND 6 CANCER 1 PROTEIN, DLC-1, HP PROTEIN, STAR-RELATED LIPID TRANSFER COMPND 7 PROTEIN 12, STARD12, START DOMAIN-CONTAINING PROTEIN 12; COMPND 8 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: DLC1, ARHGAP7, KIAA1723, STARD12; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: P050207-01; SOURCE 8 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS KEYWDS CELL-FREE PROTEIN SYNTHESIS, PROTEIN REGULATION, STRUCTURAL GENOMICS, KEYWDS 2 NPPSFA, NATIONAL PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL KEYWDS 3 ANALYSES, RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, KEYWDS 4 SIGNALING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR A.K.GORONCY,M.SATO,S.KOSHIBA,M.INOUE,T.KIGAWA,S.YOKOYAMA,RIKEN AUTHOR 2 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 3 09-MAR-22 2DKY 1 REMARK SEQADV REVDAT 2 24-FEB-09 2DKY 1 VERSN REVDAT 1 24-APR-07 2DKY 0 JRNL AUTH A.K.GORONCY,M.SATO,S.KOSHIBA,M.INOUE,T.KIGAWA,S.YOKOYAMA JRNL TITL SOLUTION STRUCTURE OF THE SAM-DOMAIN OF JRNL TITL 2 RHO-GTPASE-ACTIVATING PROTEIN 7 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 2.0.17 REMARK 3 AUTHORS : P.GUNTERT ET AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2DKY COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-APR-06. REMARK 100 THE DEPOSITION ID IS D_1000025538. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 296 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 120MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.08MM SAM DOMAIN, 20MM D-TRIS REMARK 210 -HCL, 100MM NACL, 1MM D-DTT, REMARK 210 0.02% NAN3, 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 : CYANA 2.0.17, XWINNMR 3.5, REMARK 210 NMRPIPE 20031121, NMRVIEW 5.0.4, REMARK 210 KUJIRA 0.899A REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS 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 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 PRO A 13 86.54 -69.70 REMARK 500 1 ASP A 14 118.32 -174.79 REMARK 500 1 THR A 15 39.34 36.79 REMARK 500 1 PRO A 88 93.58 -69.73 REMARK 500 2 ARG A 10 46.89 -91.68 REMARK 500 2 HIS A 58 32.50 -96.32 REMARK 500 2 LEU A 61 161.30 -45.20 REMARK 500 2 LEU A 84 -74.19 -76.49 REMARK 500 2 GLU A 85 92.22 -49.76 REMARK 500 2 SER A 90 162.28 -45.95 REMARK 500 3 SER A 2 106.79 -169.38 REMARK 500 3 MET A 16 -53.58 -134.96 REMARK 500 3 LEU A 30 -35.22 -39.39 REMARK 500 3 PHE A 35 78.71 -109.81 REMARK 500 3 SER A 52 -37.44 -38.00 REMARK 500 3 HIS A 58 40.10 -99.07 REMARK 500 3 LEU A 61 163.25 -43.13 REMARK 500 3 MET A 82 -33.74 -34.17 REMARK 500 3 GLU A 85 107.18 -170.18 REMARK 500 4 ARG A 10 63.29 -116.66 REMARK 500 4 LYS A 12 78.62 -117.72 REMARK 500 4 THR A 15 40.91 34.03 REMARK 500 4 LEU A 61 163.18 -41.66 REMARK 500 4 GLU A 85 108.02 -166.53 REMARK 500 5 HIS A 58 50.67 -105.09 REMARK 500 5 LEU A 61 164.69 -46.74 REMARK 500 5 SER A 90 154.60 -44.21 REMARK 500 6 HIS A 58 44.82 -101.12 REMARK 500 6 SER A 86 43.57 -80.16 REMARK 500 7 ARG A 10 145.12 -174.20 REMARK 500 7 THR A 15 106.09 -39.40 REMARK 500 7 LEU A 30 -39.85 -35.78 REMARK 500 7 PHE A 35 78.79 -107.63 REMARK 500 7 PHE A 45 40.35 70.90 REMARK 500 7 HIS A 58 52.61 -101.60 REMARK 500 7 LEU A 61 166.11 -49.69 REMARK 500 7 MET A 82 -25.63 -39.89 REMARK 500 7 GLU A 85 -72.15 -36.47 REMARK 500 8 SER A 5 107.13 -166.83 REMARK 500 8 LEU A 61 165.60 -49.43 REMARK 500 8 LYS A 83 -38.97 -34.39 REMARK 500 9 PHE A 45 47.83 73.87 REMARK 500 9 LEU A 61 160.51 -46.40 REMARK 500 9 MET A 82 -31.46 -35.32 REMARK 500 10 SER A 6 106.38 -166.76 REMARK 500 10 LYS A 12 54.77 35.74 REMARK 500 10 THR A 15 40.74 -96.93 REMARK 500 10 LEU A 30 -35.36 -38.83 REMARK 500 10 PHE A 35 79.00 -107.53 REMARK 500 10 HIS A 58 43.48 -98.32 REMARK 500 REMARK 500 THIS ENTRY HAS 107 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF 2DKY A 8 85 UNP Q96QB1 RHG07_HUMAN 1 78 SEQADV 2DKY GLY A 1 UNP Q96QB1 CLONING ARTIFACT SEQADV 2DKY SER A 2 UNP Q96QB1 CLONING ARTIFACT SEQADV 2DKY SER A 3 UNP Q96QB1 CLONING ARTIFACT SEQADV 2DKY GLY A 4 UNP Q96QB1 CLONING ARTIFACT SEQADV 2DKY SER A 5 UNP Q96QB1 CLONING ARTIFACT SEQADV 2DKY SER A 6 UNP Q96QB1 CLONING ARTIFACT SEQADV 2DKY GLY A 7 UNP Q96QB1 CLONING ARTIFACT SEQADV 2DKY SER A 86 UNP Q96QB1 CLONING ARTIFACT SEQADV 2DKY GLY A 87 UNP Q96QB1 CLONING ARTIFACT SEQADV 2DKY PRO A 88 UNP Q96QB1 CLONING ARTIFACT SEQADV 2DKY SER A 89 UNP Q96QB1 CLONING ARTIFACT SEQADV 2DKY SER A 90 UNP Q96QB1 CLONING ARTIFACT SEQADV 2DKY GLY A 91 UNP Q96QB1 CLONING ARTIFACT SEQRES 1 A 91 GLY SER SER GLY SER SER GLY MET CYS ARG LYS LYS PRO SEQRES 2 A 91 ASP THR MET ILE LEU THR GLN ILE GLU ALA LYS GLU ALA SEQRES 3 A 91 CYS ASP TRP LEU ARG ALA THR GLY PHE PRO GLN TYR ALA SEQRES 4 A 91 GLN LEU TYR GLU ASP PHE LEU PHE PRO ILE ASP ILE SER SEQRES 5 A 91 LEU VAL LYS ARG GLU HIS ASP PHE LEU ASP ARG ASP ALA SEQRES 6 A 91 ILE GLU ALA LEU CYS ARG ARG LEU ASN THR LEU ASN LYS SEQRES 7 A 91 CYS ALA VAL MET LYS LEU GLU SER GLY PRO SER SER GLY HELIX 1 1 THR A 15 GLY A 34 1 20 HELIX 2 2 GLN A 37 ASP A 44 1 8 HELIX 3 3 ASP A 50 HIS A 58 1 9 HELIX 4 4 ASP A 62 ALA A 80 1 19 CISPEP 1 PHE A 47 PRO A 48 1 -0.02 CISPEP 2 PHE A 47 PRO A 48 2 -0.07 CISPEP 3 PHE A 47 PRO A 48 3 0.00 CISPEP 4 PHE A 47 PRO A 48 4 -0.09 CISPEP 5 PHE A 47 PRO A 48 5 -0.06 CISPEP 6 PHE A 47 PRO A 48 6 -0.03 CISPEP 7 PHE A 47 PRO A 48 7 0.00 CISPEP 8 PHE A 47 PRO A 48 8 -0.02 CISPEP 9 PHE A 47 PRO A 48 9 -0.03 CISPEP 10 PHE A 47 PRO A 48 10 -0.05 CISPEP 11 PHE A 47 PRO A 48 11 0.01 CISPEP 12 PHE A 47 PRO A 48 12 0.00 CISPEP 13 PHE A 47 PRO A 48 13 0.02 CISPEP 14 PHE A 47 PRO A 48 14 0.03 CISPEP 15 PHE A 47 PRO A 48 15 0.01 CISPEP 16 PHE A 47 PRO A 48 16 0.03 CISPEP 17 PHE A 47 PRO A 48 17 0.01 CISPEP 18 PHE A 47 PRO A 48 18 -0.06 CISPEP 19 PHE A 47 PRO A 48 19 0.03 CISPEP 20 PHE A 47 PRO A 48 20 0.00 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