HEADER SIGNALING PROTEIN 22-MAR-01 1IAP TITLE CRYSTAL STRUCTURE OF P115RHOGEF RGRGS DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: GUANINE NUCLEOTIDE EXCHANGE FACTOR P115RHOGEF; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL RGS DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PTRCC KEYWDS P115, RHOGEF, RGS, RGRGS, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.R.SPRANG,Z.CHEN REVDAT 4 03-APR-24 1IAP 1 REMARK REVDAT 3 07-FEB-24 1IAP 1 REMARK REVDAT 2 24-FEB-09 1IAP 1 VERSN REVDAT 1 05-SEP-01 1IAP 0 JRNL AUTH Z.CHEN,C.D.WELLS,P.C.STERNWEIS,S.R.SPRANG JRNL TITL STRUCTURE OF THE RGRGS DOMAIN OF P115RHOGEF. JRNL REF NAT.STRUCT.BIOL. V. 8 805 2001 JRNL REFN ISSN 1072-8368 JRNL PMID 11524686 JRNL DOI 10.1038/NSB0901-805 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.9 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.55 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1423020.440 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 90.0 REMARK 3 NUMBER OF REFLECTIONS : 13175 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.219 REMARK 3 FREE R VALUE : 0.275 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.300 REMARK 3 FREE R VALUE TEST SET COUNT : 1352 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 81.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1754 REMARK 3 BIN R VALUE (WORKING SET) : 0.3040 REMARK 3 BIN FREE R VALUE : 0.3390 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 181 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.025 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1533 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 91 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 11.72000 REMARK 3 B22 (A**2) : -3.48000 REMARK 3 B33 (A**2) : -8.24000 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) : 0.24 REMARK 3 ESD FROM SIGMAA (A) : 0.36 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.31 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.27 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.000 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 20.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.980 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED 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 : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 48.57 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1IAP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-APR-01. REMARK 100 THE DEPOSITION ID IS D_1000013103. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-01 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 9.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9760 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13303 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 16.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.0 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.12000 REMARK 200 R SYM (I) : 0.12000 REMARK 200 FOR THE DATA SET : 12.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 79.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.48500 REMARK 200 R SYM FOR SHELL (I) : 0.48500 REMARK 200 FOR SHELL : 4.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: SE-MET STRUCTURE OF THE SAME PROTEIN SOLVED BY MAD REMARK 200 PHASING FROM A FOUR-WAVELENGTH MAD DATASET COLLECTED AT CHESS F2 REMARK 200 BEAMLINE (UNPUBLISHED DATA) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 28.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, AMMONIUM FORMATE, CHES, PH REMARK 280 9.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 18.42950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 64.08550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.71600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 64.08550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.42950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 18.71600 REMARK 290 SMTRY3 4 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: 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 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 GLN A 42 REMARK 465 ASN A 43 REMARK 465 LYS A 234 REMARK 465 SER A 235 REMARK 465 GLY A 236 REMARK 465 ASP A 237 REMARK 465 LYS A 238 REMARK 465 LYS A 239 REMARK 465 SER A 240 REMARK 465 GLY A 241 REMARK 465 ARG A 242 REMARK 465 ASN A 243 REMARK 465 PHE A 244 REMARK 465 PHE A 245 REMARK 465 ARG A 246 REMARK 465 LYS A 247 REMARK 465 LYS A 248 REMARK 465 VAL A 249 REMARK 465 MET A 250 REMARK 465 GLY A 251 REMARK 465 ASN A 252 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1AGR RELATED DB: PDB REMARK 900 1AGR CONTAINS RGS4 STRUCTURE REMARK 900 RELATED ID: 1FQJ RELATED DB: PDB REMARK 900 1FQJ CONTAINS RGS9 STRUCTURE REMARK 900 RELATED ID: 1CMZ RELATED DB: PDB REMARK 900 1CMZ CONTAINS GAIP STRUCTURE REMARK 900 RELATED ID: 1DK8 RELATED DB: PDB REMARK 900 1DK8 CONTAINS AXIN STRUCTURE DBREF 1IAP A 42 252 UNP Q92888 ARHG1_HUMAN 42 252 SEQRES 1 A 211 GLN ASN SER GLN PHE GLN SER LEU GLU GLN VAL LYS ARG SEQRES 2 A 211 ARG PRO ALA HIS LEU MET ALA LEU LEU GLN HIS VAL ALA SEQRES 3 A 211 LEU GLN PHE GLU PRO GLY PRO LEU LEU CYS CYS LEU HIS SEQRES 4 A 211 ALA ASP MET LEU GLY SER LEU GLY PRO LYS GLU ALA LYS SEQRES 5 A 211 LYS ALA PHE LEU ASP PHE TYR HIS SER PHE LEU GLU LYS SEQRES 6 A 211 THR ALA VAL LEU ARG VAL PRO VAL PRO PRO ASN VAL ALA SEQRES 7 A 211 PHE GLU LEU ASP ARG THR ARG ALA ASP LEU ILE SER GLU SEQRES 8 A 211 ASP VAL GLN ARG ARG PHE VAL GLN GLU VAL VAL GLN SER SEQRES 9 A 211 GLN GLN VAL ALA VAL GLY ARG GLN LEU GLU ASP PHE ARG SEQRES 10 A 211 SER LYS ARG LEU MET GLY MET THR PRO TRP GLU GLN GLU SEQRES 11 A 211 LEU ALA GLN LEU GLU ALA TRP VAL GLY ARG ASP ARG ALA SEQRES 12 A 211 SER TYR GLU ALA ARG GLU ARG HIS VAL ALA GLU ARG LEU SEQRES 13 A 211 LEU MET HIS LEU GLU GLU MET GLN HIS THR ILE SER THR SEQRES 14 A 211 ASP GLU GLU LYS SER ALA ALA VAL VAL ASN ALA ILE GLY SEQRES 15 A 211 LEU TYR MET ARG HIS LEU GLY VAL ARG THR LYS SER GLY SEQRES 16 A 211 ASP LYS LYS SER GLY ARG ASN PHE PHE ARG LYS LYS VAL SEQRES 17 A 211 MET GLY ASN FORMUL 2 HOH *91(H2 O) HELIX 1 1 SER A 48 LYS A 53 1 6 HELIX 2 2 ARG A 55 PHE A 70 1 16 HELIX 3 3 PRO A 72 GLY A 85 1 14 HELIX 4 4 GLY A 88 LEU A 104 1 17 HELIX 5 5 PRO A 115 ASP A 123 1 9 HELIX 6 6 SER A 131 SER A 145 1 15 HELIX 7 7 GLN A 146 MET A 163 1 18 HELIX 8 8 TRP A 168 ALA A 177 1 10 HELIX 9 9 ASP A 182 MET A 204 1 23 HELIX 10 10 GLN A 205 ILE A 208 5 4 HELIX 11 11 ASP A 211 LEU A 229 1 19 CRYST1 36.859 37.432 128.171 90.00 90.00 90.00 P 21 21 21 4 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 0.027130 0.000000 0.000000 0.00000 SCALE2 0.000000 0.026715 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007802 0.00000