PDB Short entry for 2COC HEADER SIGNALING PROTEIN 17-MAY-05 2COC TITLE SOLUTION STRUCTURE OF THE C-TERMINAL PH DOMAIN OF FYVE, RHOGEF AND PH TITLE 2 DOMAIN CONTAINING PROTEIN 3 (FGD3) FROM HUMAN COMPND MOL_ID: 1; COMPND 2 MOLECULE: FYVE, RHOGEF AND PH DOMAIN CONTAINING PROTEIN 3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PH DOMAIN; COMPND 5 SYNONYM: ZINC FINGER FYVE DOMAIN CONTAINING PROTEIN 5; 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: FGD3; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: P050125-03; SOURCE 8 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS KEYWDS FYVE, RHOGEF AND PH DOMAIN CONTAINING PROTEIN 3, PH DOMAIN, KEYWDS 2 STRUCTURAL GENOMICS, NPPSFA, NATIONAL PROJECT ON PROTEIN STRUCTURAL KEYWDS 3 AND FUNCTIONAL ANALYSES, RIKEN STRUCTURAL GENOMICS/PROTEOMICS KEYWDS 4 INITIATIVE, RSGI, SIGNALING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR H.LI,T.TOMIZAWA,N.TOCHIO,Y.MUTO,S.KOSHIBA,M.INOUE,T.KIGAWA, AUTHOR 2 S.YOKOYAMA,RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 3 09-MAR-22 2COC 1 REMARK SEQADV REVDAT 2 24-FEB-09 2COC 1 VERSN REVDAT 1 17-NOV-05 2COC 0 JRNL AUTH H.LI,T.TOMIZAWA,N.TOCHIO,Y.MUTO,S.KOSHIBA,M.INOUE,T.KIGAWA, JRNL AUTH 2 S.YOKOYAMA JRNL TITL SOLUTION STRUCTURE OF THE C-TERMINAL PH DOMAIN OF FYVE, JRNL TITL 2 RHOGEF AND PH DOMAIN CONTAINING PROTEIN 3 (FGD3) FROM HUMAN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 2.6, CYANA 2.0.17 REMARK 3 AUTHORS : BRUKER (XWINNMR), GUNTERT, P. (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2COC COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-MAY-05. REMARK 100 THE DEPOSITION ID IS D_1000024444. 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 : 1.20MM PH DOMAIN U-13C, 15N; REMARK 210 20MM D-TRIS-HCL(PH7.0); 100MM REMARK 210 NACL; 1MM D-DTT; 0.02% NAN3; 90% REMARK 210 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 20031121, NMRVIEW 5.0.4, REMARK 210 KUJIRA 0.9295, 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 LEAST 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 SER A 8 139.28 -38.73 REMARK 500 1 GLU A 21 -56.45 -121.84 REMARK 500 1 LEU A 49 145.45 -35.73 REMARK 500 1 GLU A 67 166.64 -46.27 REMARK 500 1 ARG A 68 44.06 -102.87 REMARK 500 1 SER A 110 92.40 -67.90 REMARK 500 2 SER A 5 42.81 -103.43 REMARK 500 2 GLU A 21 -53.91 -128.20 REMARK 500 2 LEU A 49 103.34 -43.21 REMARK 500 2 PRO A 56 -17.11 -48.00 REMARK 500 2 LEU A 69 -179.85 -58.89 REMARK 500 2 SER A 83 112.02 -162.46 REMARK 500 3 SER A 5 45.98 -84.33 REMARK 500 3 GLU A 21 -68.03 -97.48 REMARK 500 3 PRO A 63 174.61 -48.13 REMARK 500 3 HIS A 106 109.10 -34.55 REMARK 500 4 GLU A 21 -44.67 -131.54 REMARK 500 4 LEU A 49 96.98 -33.67 REMARK 500 4 PRO A 56 -18.61 -47.99 REMARK 500 4 LEU A 69 175.79 -48.59 REMARK 500 4 SER A 83 118.37 -160.81 REMARK 500 4 SER A 110 -50.77 -126.48 REMARK 500 5 SER A 6 39.06 -92.71 REMARK 500 5 PRO A 56 -17.33 -47.94 REMARK 500 6 SER A 44 -61.91 -122.32 REMARK 500 6 LEU A 69 166.65 -43.67 REMARK 500 6 SER A 111 85.56 -52.94 REMARK 500 7 SER A 2 49.26 -86.07 REMARK 500 7 SER A 5 83.42 -65.03 REMARK 500 7 GLU A 21 -63.75 -122.60 REMARK 500 7 LEU A 69 173.91 -58.26 REMARK 500 7 PRO A 109 162.66 -45.58 REMARK 500 8 SER A 44 42.12 -90.55 REMARK 500 8 LEU A 49 99.80 -37.95 REMARK 500 8 GLU A 67 166.01 -43.86 REMARK 500 8 ASP A 70 -61.91 -104.85 REMARK 500 8 SER A 71 -175.08 -63.10 REMARK 500 8 SER A 89 -38.27 -39.84 REMARK 500 8 PRO A 109 47.22 -74.91 REMARK 500 9 SER A 2 46.96 -86.65 REMARK 500 9 LEU A 49 109.42 -55.84 REMARK 500 9 PRO A 56 -17.26 -47.95 REMARK 500 9 LEU A 69 176.47 -49.05 REMARK 500 9 PRO A 109 172.42 -47.02 REMARK 500 10 GLU A 21 -56.17 -128.22 REMARK 500 10 PRO A 56 -17.91 -47.95 REMARK 500 10 PRO A 63 173.34 -48.29 REMARK 500 10 SER A 83 113.46 -161.62 REMARK 500 10 SER A 111 -44.29 -131.72 REMARK 500 11 SER A 2 -51.73 -133.15 REMARK 500 REMARK 500 THIS ENTRY HAS 113 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 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HSI002021744.1 RELATED DB: TARGETDB DBREF 2COC A 8 106 UNP Q5JSP0 FGD3_HUMAN 605 703 SEQADV 2COC GLY A 1 UNP Q5JSP0 CLONING ARTIFACT SEQADV 2COC SER A 2 UNP Q5JSP0 CLONING ARTIFACT SEQADV 2COC SER A 3 UNP Q5JSP0 CLONING ARTIFACT SEQADV 2COC GLY A 4 UNP Q5JSP0 CLONING ARTIFACT SEQADV 2COC SER A 5 UNP Q5JSP0 CLONING ARTIFACT SEQADV 2COC SER A 6 UNP Q5JSP0 CLONING ARTIFACT SEQADV 2COC GLY A 7 UNP Q5JSP0 CLONING ARTIFACT SEQADV 2COC SER A 107 UNP Q5JSP0 CLONING ARTIFACT SEQADV 2COC GLY A 108 UNP Q5JSP0 CLONING ARTIFACT SEQADV 2COC PRO A 109 UNP Q5JSP0 CLONING ARTIFACT SEQADV 2COC SER A 110 UNP Q5JSP0 CLONING ARTIFACT SEQADV 2COC SER A 111 UNP Q5JSP0 CLONING ARTIFACT SEQADV 2COC GLY A 112 UNP Q5JSP0 CLONING ARTIFACT SEQRES 1 A 112 GLY SER SER GLY SER SER GLY SER LEU LEU CYS GLY PRO SEQRES 2 A 112 LEU ARG LEU SER GLU SER GLY GLU THR TRP SER GLU VAL SEQRES 3 A 112 TRP ALA ALA ILE PRO MET SER ASP PRO GLN VAL LEU HIS SEQRES 4 A 112 LEU GLN GLY GLY SER GLN ASP GLY ARG LEU PRO ARG THR SEQRES 5 A 112 ILE PRO LEU PRO SER CYS LYS LEU SER VAL PRO ASP PRO SEQRES 6 A 112 GLU GLU ARG LEU ASP SER GLY HIS VAL TRP LYS LEU GLN SEQRES 7 A 112 TRP ALA LYS GLN SER TRP TYR LEU SER ALA SER SER ALA SEQRES 8 A 112 GLU LEU GLN GLN GLN TRP LEU GLU THR LEU SER THR ALA SEQRES 9 A 112 ALA HIS SER GLY PRO SER SER GLY HELIX 1 1 ALA A 91 ALA A 105 5 15 SHEET 1 A 7 ARG A 51 ILE A 53 0 SHEET 2 A 7 VAL A 37 GLN A 41 -1 SHEET 3 A 7 TRP A 23 PRO A 31 -1 SHEET 4 A 7 CYS A 11 SER A 17 -1 SHEET 5 A 7 GLN A 82 ALA A 88 -1 SHEET 6 A 7 HIS A 73 TRP A 79 -1 SHEET 7 A 7 LYS A 59 SER A 61 -1 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