HEADER SIGNALING PROTEIN 20-MAY-05 2CRW TITLE SOLUTION STRUCTURE OF THE ARFGAP DOMAIN OF ADP-RIBOSYLATION FACTOR TITLE 2 GTPASEACTIVATING PROTEIN 3 (ARFGAP 3) COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADP-RIBOSYLATION FACTOR GTPASE-ACTIVATING PROTEIN 3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ARFGAP DOMAIN; COMPND 5 SYNONYM: ARF GAP 3; 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: ARFGAP3, ARFGAP1; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: P040628-13; SOURCE 8 OTHER_DETAILS: CELL FREE PROTEIN SYNTHESIS KEYWDS ARFGAP DOMAIN, ADP-RIBOSYLATION FACTOR GTPASE-ACTIVATING PROTEIN 3, KEYWDS 2 ARF GAP 3, STRUCTURAL GENOMICS, NPPSFA, NATIONAL PROJECT ON PROTEIN KEYWDS 3 STRUCTURAL AND FUNCTIONAL ANALYSES, RIKEN STRUCTURAL KEYWDS 4 GENOMICS/PROTEOMICS INITIATIVE, RSGI, SIGNALING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR H.P.ZHANG,F.HAYASHI,S.YOKOYAMA,RIKEN STRUCTURAL GENOMICS/PROTEOMICS AUTHOR 2 INITIATIVE (RSGI) REVDAT 3 09-MAR-22 2CRW 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 2CRW 1 VERSN REVDAT 1 20-NOV-05 2CRW 0 JRNL AUTH H.P.ZHANG,F.HAYASHI,S.YOKOYAMA JRNL TITL SOLUTION STRUCTURE OF THE ARFGAP DOMAIN OF ADP-RIBOSYLATION JRNL TITL 2 FACTOR GTPASEACTIVATING PROTEIN 3 (ARFGAP 3) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 6.1C, CYANA 2.0.17 REMARK 3 AUTHORS : VARIAN (VNMR), GUNTERT,P. (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2CRW COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 31-MAY-05. REMARK 100 THE DEPOSITION ID IS D_1000024554. 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-LABELED PROTEIN; REMARK 210 20MM D-TRIS-HCL; 100MM NACL; 1MM REMARK 210 D-DTT;0.02% NAN3, 0.01MM ZNCL2; REMARK 210 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; 900 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 20031121, NMRVIEW 5.04, REMARK 210 KUJIRA 0.9296, CYANA 2.0.17 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 : 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: SPECTROMETER_ID 1 FOR 3D_15N_SEPARATED_NOESY; REMARK 210 SPECTROMETED_ID 2 FOR 3D_13C_SEPARATED_NOESY 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 CYS A 32 106.36 -35.20 REMARK 500 1 ASP A 34 -70.72 -75.58 REMARK 500 1 PRO A 40 80.59 -69.71 REMARK 500 1 ILE A 53 -34.44 -33.23 REMARK 500 1 SER A 56 -36.18 -33.45 REMARK 500 1 VAL A 64 -31.59 -38.79 REMARK 500 1 LEU A 74 -67.15 -95.88 REMARK 500 1 CYS A 85 -35.23 -37.09 REMARK 500 1 SER A 95 -39.07 -39.55 REMARK 500 1 ASP A 107 138.81 -36.29 REMARK 500 1 ALA A 128 -32.18 -37.16 REMARK 500 1 ASP A 138 102.09 -34.41 REMARK 500 1 LEU A 139 100.14 -43.24 REMARK 500 1 SER A 148 106.63 -49.49 REMARK 500 2 SER A 6 45.99 -96.70 REMARK 500 2 MET A 8 42.26 -80.70 REMARK 500 2 PRO A 27 1.57 -69.82 REMARK 500 2 CYS A 32 112.67 -35.28 REMARK 500 2 ASP A 34 -71.34 -70.76 REMARK 500 2 PRO A 40 80.23 -69.81 REMARK 500 2 ILE A 53 -38.41 -32.80 REMARK 500 2 ASN A 77 46.83 -77.41 REMARK 500 2 TRP A 80 -37.69 -34.56 REMARK 500 2 SER A 93 -64.08 -29.81 REMARK 500 2 SER A 95 -33.11 -38.92 REMARK 500 2 ASP A 107 171.35 -49.25 REMARK 500 2 HIS A 135 -45.42 -133.16 REMARK 500 2 LEU A 141 109.05 -34.75 REMARK 500 2 PRO A 146 90.02 -69.67 REMARK 500 3 CYS A 32 104.78 -37.57 REMARK 500 3 ASP A 34 -71.60 -74.02 REMARK 500 3 PRO A 40 80.51 -69.75 REMARK 500 3 ILE A 53 -33.67 -33.91 REMARK 500 3 ASP A 54 -72.23 -69.00 REMARK 500 3 SER A 56 -37.65 -32.57 REMARK 500 3 VAL A 64 -29.46 -38.60 REMARK 500 3 GLU A 73 -73.79 -76.69 REMARK 500 3 VAL A 88 -18.08 -49.44 REMARK 500 3 SER A 95 -39.92 -35.61 REMARK 500 3 SER A 104 44.28 -90.21 REMARK 500 3 ASP A 107 133.76 -34.34 REMARK 500 3 ALA A 128 -38.92 -35.19 REMARK 500 3 ARG A 133 -27.53 -39.55 REMARK 500 3 LYS A 134 158.95 -38.62 REMARK 500 3 HIS A 135 99.96 -32.17 REMARK 500 3 ASP A 138 109.38 -33.18 REMARK 500 3 LEU A 139 109.12 -43.15 REMARK 500 3 TRP A 140 -36.15 -33.33 REMARK 500 4 MET A 8 135.35 -38.43 REMARK 500 4 ILE A 19 -36.76 -37.15 REMARK 500 REMARK 500 THIS ENTRY HAS 328 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 32 SG REMARK 620 2 CYS A 35 SG 102.3 REMARK 620 3 CYS A 52 SG 119.2 102.9 REMARK 620 4 CYS A 55 SG 108.6 118.7 105.7 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HSS001001677.1 RELATED DB: TARGETDB DBREF 2CRW A 8 143 UNP Q9NP61 ARFG3_HUMAN 1 136 SEQADV 2CRW GLY A 1 UNP Q9NP61 CLONING ARTIFACT SEQADV 2CRW SER A 2 UNP Q9NP61 CLONING ARTIFACT SEQADV 2CRW SER A 3 UNP Q9NP61 CLONING ARTIFACT SEQADV 2CRW GLY A 4 UNP Q9NP61 CLONING ARTIFACT SEQADV 2CRW SER A 5 UNP Q9NP61 CLONING ARTIFACT SEQADV 2CRW SER A 6 UNP Q9NP61 CLONING ARTIFACT SEQADV 2CRW GLY A 7 UNP Q9NP61 CLONING ARTIFACT SEQADV 2CRW SER A 144 UNP Q9NP61 CLONING ARTIFACT SEQADV 2CRW GLY A 145 UNP Q9NP61 CLONING ARTIFACT SEQADV 2CRW PRO A 146 UNP Q9NP61 CLONING ARTIFACT SEQADV 2CRW SER A 147 UNP Q9NP61 CLONING ARTIFACT SEQADV 2CRW SER A 148 UNP Q9NP61 CLONING ARTIFACT SEQADV 2CRW GLY A 149 UNP Q9NP61 CLONING ARTIFACT SEQRES 1 A 149 GLY SER SER GLY SER SER GLY MET GLY ASP PRO SER LYS SEQRES 2 A 149 GLN ASP ILE LEU THR ILE PHE LYS ARG LEU ARG SER VAL SEQRES 3 A 149 PRO THR ASN LYS VAL CYS PHE ASP CYS GLY ALA LYS ASN SEQRES 4 A 149 PRO SER TRP ALA SER ILE THR TYR GLY VAL PHE LEU CYS SEQRES 5 A 149 ILE ASP CYS SER GLY SER HIS ARG SER LEU GLY VAL HIS SEQRES 6 A 149 LEU SER PHE ILE ARG SER THR GLU LEU ASP SER ASN TRP SEQRES 7 A 149 SER TRP PHE GLN LEU ARG CYS MET GLN VAL GLY GLY ASN SEQRES 8 A 149 ALA SER ALA SER SER PHE PHE HIS GLN HIS GLY CYS SER SEQRES 9 A 149 THR ASN ASP THR ASN ALA LYS TYR ASN SER ARG ALA ALA SEQRES 10 A 149 GLN LEU TYR ARG GLU LYS ILE LYS SER LEU ALA SER GLN SEQRES 11 A 149 ALA THR ARG LYS HIS GLY THR ASP LEU TRP LEU ASP SER SEQRES 12 A 149 SER GLY PRO SER SER GLY HET ZN A 401 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ HELIX 1 1 LYS A 13 SER A 25 1 13 HELIX 2 2 ILE A 53 LEU A 62 1 10 HELIX 3 3 TRP A 80 GLN A 87 1 8 HELIX 4 4 ASN A 91 HIS A 101 1 11 HELIX 5 5 THR A 108 LYS A 111 1 4 HELIX 6 6 ARG A 115 ARG A 133 1 19 SHEET 1 A 3 VAL A 49 PHE A 50 0 SHEET 2 A 3 ALA A 43 SER A 44 -1 N SER A 44 O VAL A 49 SHEET 3 A 3 ILE A 69 ARG A 70 -1 O ARG A 70 N ALA A 43 LINK SG CYS A 32 ZN ZN A 401 1555 1555 2.32 LINK SG CYS A 35 ZN ZN A 401 1555 1555 2.32 LINK SG CYS A 52 ZN ZN A 401 1555 1555 2.32 LINK SG CYS A 55 ZN ZN A 401 1555 1555 2.34 SITE 1 AC1 4 CYS A 32 CYS A 35 CYS A 52 CYS A 55 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