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 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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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
(ATOM LINES ARE NOT SHOWN.)
END