HEADER SIGNALING PROTEIN 28-MAY-04 1WGY TITLE RA DOMAIN OF GUANINE NUCLEOTIDE EXCHANGE FACTOR FOR RAP1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAP GUANINE NUCLEOTIDE EXCHANGE FACTOR 5; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RA DOMAIN; COMPND 5 SYNONYM: GUANINE NUCLEOTIDE EXCHANGE FACTOR FOR RAP1, RELATED TO COMPND 6 EPAC, REPAC, M-RAS-REGULATED RAP GEF, MR-GEF; 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: KAZUSA CDNA HA06833; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: P030804-93; SOURCE 8 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS KEYWDS UBIQUITIN FOLD, RA, GUANINE NUCLEOTIDE EXCHANGE, RAP1, RIKEN KEYWDS 2 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, STRUCTURAL KEYWDS 3 GENOMICS, SIGNALING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR T.NAGASHIMA,N.TOCHIO,T.KIGAWA,F.HAYASHI,S.YOKOYAMA,RIKEN STRUCTURAL AUTHOR 2 GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 3 02-MAR-22 1WGY 1 REMARK SEQADV REVDAT 2 24-FEB-09 1WGY 1 VERSN REVDAT 1 28-NOV-04 1WGY 0 JRNL AUTH T.NAGASHIMA,N.TOCHIO,T.KIGAWA,F.HAYASHI,S.YOKOYAMA JRNL TITL RA DOMAIN OF GUANINE NUCLEOTIDE EXCHANGE FACTOR FOR RAP1 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 1.0.7 REMARK 3 AUTHORS : BRUKER (XWINNMR), GUENTERT, P. (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1WGY COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-JUN-04. REMARK 100 THE DEPOSITION ID IS D_1000023568. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 296 REMARK 210 PH : 7.5 REMARK 210 IONIC STRENGTH : 120MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.04MM 13C/15N-LABELED PROTEIN; REMARK 210 20MM D-TRIS, 100MM NACL, 1MM D- REMARK 210 DTT, 0.02% NAN3 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N 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 20020425, NMRVIEW 5.0.4, REMARK 210 KUJIRA 0.8992, CYANA 1.0.7 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, 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O ILE A 35 H VAL A 39 1.56 REMARK 500 H CYS A 12 O VAL A 24 1.56 REMARK 500 O ALA A 32 H ILE A 35 1.57 REMARK 500 H VAL A 53 O TYR A 82 1.60 REMARK 500 REMARK 500 REMARK: NULL 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 2 154.88 67.44 REMARK 500 1 SER A 3 101.93 -166.92 REMARK 500 1 GLU A 8 40.96 35.22 REMARK 500 1 THR A 17 -139.39 -113.81 REMARK 500 1 GLN A 44 59.94 73.92 REMARK 500 1 LEU A 64 -157.97 -127.36 REMARK 500 1 ILE A 71 70.88 -113.33 REMARK 500 1 LYS A 73 82.07 54.00 REMARK 500 1 LEU A 75 82.26 -161.72 REMARK 500 1 GLU A 76 108.51 -161.95 REMARK 500 1 SER A 78 157.20 69.66 REMARK 500 1 ASN A 93 141.05 61.84 REMARK 500 1 PRO A 94 -166.23 -75.03 REMARK 500 1 GLU A 97 -59.51 -175.28 REMARK 500 1 ASN A 98 86.78 41.18 REMARK 500 1 SER A 103 90.07 39.56 REMARK 500 2 SER A 2 -58.52 -141.37 REMARK 500 2 SER A 5 72.18 63.29 REMARK 500 2 SER A 6 -177.05 -170.36 REMARK 500 2 THR A 17 -139.38 -117.02 REMARK 500 2 GLN A 44 60.39 71.89 REMARK 500 2 LEU A 64 -159.58 -130.15 REMARK 500 2 LEU A 69 128.94 84.70 REMARK 500 2 VAL A 70 45.16 -106.93 REMARK 500 2 ILE A 71 50.10 178.27 REMARK 500 2 SER A 72 99.78 -179.44 REMARK 500 2 LYS A 73 47.90 -149.88 REMARK 500 2 LEU A 75 -51.10 -163.32 REMARK 500 2 GLU A 76 155.63 64.15 REMARK 500 2 ALA A 77 178.73 51.77 REMARK 500 2 SER A 78 165.42 62.35 REMARK 500 2 LEU A 88 99.51 -41.28 REMARK 500 2 ALA A 89 -27.49 161.42 REMARK 500 2 ASP A 90 -59.72 72.77 REMARK 500 2 THR A 91 176.85 -52.27 REMARK 500 2 ALA A 96 76.47 44.06 REMARK 500 2 ASN A 98 -55.40 -136.83 REMARK 500 3 SER A 5 98.20 -62.68 REMARK 500 3 SER A 6 -58.73 -167.72 REMARK 500 3 GLU A 8 50.60 -169.24 REMARK 500 3 THR A 17 -139.24 -115.48 REMARK 500 3 SER A 29 46.96 -147.33 REMARK 500 3 GLN A 44 60.67 73.91 REMARK 500 3 SER A 58 -65.20 70.93 REMARK 500 3 LEU A 64 -159.53 -95.32 REMARK 500 3 ILE A 71 50.67 -155.87 REMARK 500 3 LEU A 75 48.19 -172.85 REMARK 500 3 ASP A 87 -75.82 -171.94 REMARK 500 3 ALA A 89 -143.51 51.72 REMARK 500 3 ASP A 90 31.35 -96.28 REMARK 500 REMARK 500 THIS ENTRY HAS 375 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HSK002000269.1 RELATED DB: TARGETDB DBREF 1WGY A 8 98 UNP Q92565 RPGF5_HUMAN 241 331 SEQADV 1WGY GLY A 1 UNP Q92565 CLONING ARTIFACT SEQADV 1WGY SER A 2 UNP Q92565 CLONING ARTIFACT SEQADV 1WGY SER A 3 UNP Q92565 CLONING ARTIFACT SEQADV 1WGY GLY A 4 UNP Q92565 CLONING ARTIFACT SEQADV 1WGY SER A 5 UNP Q92565 CLONING ARTIFACT SEQADV 1WGY SER A 6 UNP Q92565 CLONING ARTIFACT SEQADV 1WGY GLY A 7 UNP Q92565 CLONING ARTIFACT SEQADV 1WGY SER A 99 UNP Q92565 CLONING ARTIFACT SEQADV 1WGY GLY A 100 UNP Q92565 CLONING ARTIFACT SEQADV 1WGY PRO A 101 UNP Q92565 CLONING ARTIFACT SEQADV 1WGY SER A 102 UNP Q92565 CLONING ARTIFACT SEQADV 1WGY SER A 103 UNP Q92565 CLONING ARTIFACT SEQADV 1WGY GLY A 104 UNP Q92565 CLONING ARTIFACT SEQRES 1 A 104 GLY SER SER GLY SER SER GLY GLU GLU ILE PHE CYS HIS SEQRES 2 A 104 VAL TYR ILE THR GLU HIS SER TYR VAL SER VAL LYS ALA SEQRES 3 A 104 LYS VAL SER SER ILE ALA GLN GLU ILE LEU LYS VAL VAL SEQRES 4 A 104 ALA GLU LYS ILE GLN TYR ALA GLU GLU ASP LEU ALA LEU SEQRES 5 A 104 VAL ALA ILE THR PHE SER GLY GLU LYS HIS GLU LEU GLN SEQRES 6 A 104 PRO ASN ASP LEU VAL ILE SER LYS SER LEU GLU ALA SER SEQRES 7 A 104 GLY ARG ILE TYR VAL TYR ARG LYS ASP LEU ALA ASP THR SEQRES 8 A 104 LEU ASN PRO PHE ALA GLU ASN SER GLY PRO SER SER GLY HELIX 1 1 ALA A 32 GLN A 44 1 13 HELIX 2 2 ALA A 46 GLU A 48 5 3 SHEET 1 A 4 TYR A 21 VAL A 24 0 SHEET 2 A 4 CYS A 12 TYR A 15 -1 N CYS A 12 O VAL A 24 SHEET 3 A 4 ARG A 80 ARG A 85 1 O ILE A 81 N TYR A 15 SHEET 4 A 4 LEU A 50 ILE A 55 -1 N VAL A 53 O TYR A 82 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