HEADER SIGNALING PROTEIN 29-SEP-06 2IJE TITLE CRYSTAL STRUCTURE OF THE CDC25 DOMAIN OF RASGRF1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GUANINE NUCLEOTIDE-RELEASING PROTEIN; COMPND 3 CHAIN: S; COMPND 4 FRAGMENT: CDC25 DOMAIN (RESIDUES 1028-1262); COMPND 5 SYNONYM: GNRP, RAS-SPECIFIC NUCLEOTIDE EXCHANGE FACTOR CDC25, COMPND 6 CDC25MM; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: 19417; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 DE3*; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX-6P-3 KEYWDS RASGRF1, CDC25 DOMAIN, RAS GUANINE NUCLEOTIDE RELEASING FACTOR, RAS- KEYWDS 2 SPECIFIC NUCLEOTIDE EXCHANGE FACTOR, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.S.FREEDMAN,J.KURIYAN REVDAT 6 30-AUG-23 2IJE 1 REMARK SEQADV REVDAT 5 30-APR-14 2IJE 1 REMARK REVDAT 4 13-JUL-11 2IJE 1 VERSN REVDAT 3 24-FEB-09 2IJE 1 VERSN REVDAT 2 21-NOV-06 2IJE 1 JRNL REVDAT 1 31-OCT-06 2IJE 0 JRNL AUTH T.S.FREEDMAN,H.SONDERMANN,G.D.FRIEDLAND,T.KORTEMME, JRNL AUTH 2 D.BAR-SAGI,S.MARQUSEE,J.KURIYAN JRNL TITL A RAS-INDUCED CONFORMATIONAL SWITCH IN THE RAS ACTIVATOR SON JRNL TITL 2 OF SEVENLESS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 103 16692 2006 JRNL REFN ISSN 0027-8424 JRNL PMID 17075039 JRNL DOI 10.1073/PNAS.0608127103 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.0 REMARK 3 NUMBER OF REFLECTIONS : 15478 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1533 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.22 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2721 REMARK 3 BIN FREE R VALUE : 0.3412 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 52 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1934 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 163 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.23700 REMARK 3 B22 (A**2) : 5.95900 REMARK 3 B33 (A**2) : -3.72200 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.195 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2IJE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-OCT-06. REMARK 100 THE DEPOSITION ID IS D_1000039644. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-MAY-05 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 5.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9740 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17115 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.08900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.90 REMARK 200 R MERGE FOR SHELL (I) : 0.54100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASES REMARK 200 STARTING MODEL: PDB ENTRY 1NVV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1:1 MIXTURE OF WELL SOLUTION: 0.1 M REMARK 280 SODIUM ACETATE, PH 5.2, 3% PEG 4000, 0.5% BETA-OCTYLGLUCOSIDE. REMARK 280 PROTEIN STOCK: 10 MG/ML RASGRF1, 10% GLYCEROL, 5 MM TCEP, 25 MM REMARK 280 TRIS, PH 8.0, 200 MM SODIUM CHLORIDE. CRYOPROTECTION: DIP IN REMARK 280 WELL SOLUTION WITH 30% SUCROSE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.15150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 55.15150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 37.71500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 38.90050 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 37.71500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 38.90050 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 55.15150 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 37.71500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 38.90050 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 55.15150 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 37.71500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 38.90050 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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: S 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 LEU S 1260 REMARK 465 PRO S 1261 REMARK 465 THR S 1262 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 GLN S1054 45.11 34.58 REMARK 500 ASN S1170 47.83 -101.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL S 170 DBREF 2IJE S 1028 1262 UNP P27671 GNRP_MOUSE 1028 1262 SEQADV 2IJE GLY S 1023 UNP P27671 CLONING ARTIFACT SEQADV 2IJE PRO S 1024 UNP P27671 CLONING ARTIFACT SEQADV 2IJE LEU S 1025 UNP P27671 CLONING ARTIFACT SEQADV 2IJE GLY S 1026 UNP P27671 CLONING ARTIFACT SEQADV 2IJE SER S 1027 UNP P27671 CLONING ARTIFACT SEQRES 1 S 240 GLY PRO LEU GLY SER ALA LEU GLU ILE ALA GLU GLN LEU SEQRES 2 S 240 THR LEU LEU ASP HIS LEU VAL PHE LYS SER ILE PRO TYR SEQRES 3 S 240 GLU GLU PHE PHE GLY GLN GLY TRP MET LYS ALA GLU LYS SEQRES 4 S 240 TYR GLU ARG THR PRO TYR ILE MET LYS THR THR LYS HIS SEQRES 5 S 240 PHE ASN HIS VAL SER ASN PHE ILE ALA SER GLU ILE ILE SEQRES 6 S 240 ARG ASN GLU ASP ILE SER ALA ARG ALA SER ALA ILE GLU SEQRES 7 S 240 LYS TRP VAL ALA VAL ALA ASP ILE CYS ARG CYS LEU HIS SEQRES 8 S 240 ASN TYR ASN ALA VAL LEU GLU ILE THR SER SER ILE ASN SEQRES 9 S 240 ARG SER ALA ILE PHE ARG LEU LYS LYS THR TRP LEU LYS SEQRES 10 S 240 VAL SER LYS GLN THR LYS SER LEU LEU ASP LYS LEU GLN SEQRES 11 S 240 LYS LEU VAL SER SER ASP GLY ARG PHE LYS ASN LEU ARG SEQRES 12 S 240 GLU SER LEU ARG ASN CYS ASP PRO PRO CYS VAL PRO TYR SEQRES 13 S 240 LEU GLY MET TYR LEU THR ASP LEU VAL PHE ILE GLU GLU SEQRES 14 S 240 GLY THR PRO ASN TYR THR GLU ASP GLY LEU VAL ASN PHE SEQRES 15 S 240 SER LYS MET ARG MET ILE SER HIS ILE ILE ARG GLU ILE SEQRES 16 S 240 ARG GLN PHE GLN GLN THR THR TYR LYS ILE ASP PRO GLN SEQRES 17 S 240 PRO LYS VAL ILE GLN TYR LEU LEU ASP GLU SER PHE MET SEQRES 18 S 240 LEU ASP GLU GLU SER LEU TYR GLU SER SER LEU LEU ILE SEQRES 19 S 240 GLU PRO LYS LEU PRO THR HET GOL S 170 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL C3 H8 O3 FORMUL 3 HOH *163(H2 O) HELIX 1 1 GLY S 1023 SER S 1045 1 23 HELIX 2 2 PRO S 1047 LYS S 1058 5 12 HELIX 3 3 GLU S 1060 THR S 1065 1 6 HELIX 4 4 THR S 1065 ARG S 1088 1 24 HELIX 5 5 ASP S 1091 LEU S 1112 1 22 HELIX 6 6 ASN S 1114 ASN S 1126 1 13 HELIX 7 7 ARG S 1127 ARG S 1132 1 6 HELIX 8 8 LEU S 1133 LYS S 1139 1 7 HELIX 9 9 SER S 1141 VAL S 1155 1 15 HELIX 10 10 SER S 1157 ASN S 1170 1 14 HELIX 11 11 TYR S 1178 THR S 1193 1 16 HELIX 12 12 ASN S 1203 THR S 1223 1 21 HELIX 13 13 GLN S 1230 ASP S 1239 1 10 HELIX 14 14 ASP S 1245 GLU S 1257 1 13 CISPEP 1 PRO S 1173 PRO S 1174 0 0.09 SITE 1 AC1 9 ILE S1087 ARG S1088 ASN S1089 GLU S1090 SITE 2 AC1 9 ARG S1095 LEU S1201 VAL S1202 PHE S1204 SITE 3 AC1 9 ILE S1256 CRYST1 75.430 77.801 110.303 90.00 90.00 90.00 C 2 2 21 8 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 0.013257 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012853 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009066 0.00000