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- PDB-1iap: CRYSTAL STRUCTURE OF P115RHOGEF RGRGS DOMAIN -

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Entry
Database: PDB / ID: 1iap
TitleCRYSTAL STRUCTURE OF P115RHOGEF RGRGS DOMAIN
ComponentsGUANINE NUCLEOTIDE EXCHANGE FACTOR P115RHOGEF
KeywordsSIGNALING PROTEIN / p115 / RhoGEF / RGS / RGRGS
Function / homology
Function and homology information


Rho-activating G protein-coupled receptor signaling pathway / regulation of small GTPase mediated signal transduction / RHOB GTPase cycle / NRAGE signals death through JNK / RHOC GTPase cycle / RHOA GTPase cycle / Rho protein signal transduction / GTPase activator activity / guanyl-nucleotide exchange factor activity / G protein-coupled receptor binding ...Rho-activating G protein-coupled receptor signaling pathway / regulation of small GTPase mediated signal transduction / RHOB GTPase cycle / NRAGE signals death through JNK / RHOC GTPase cycle / RHOA GTPase cycle / Rho protein signal transduction / GTPase activator activity / guanyl-nucleotide exchange factor activity / G protein-coupled receptor binding / G alpha (12/13) signalling events / G protein-coupled receptor signaling pathway / RNA binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
p115RhoGEF, RGS domain / Regulator of G protein signalling-like domain / Regulator of G protein signalling-like domain / ARHGEF1-like, PH domain / PH domain / Regulator of G-protein Signalling 4, domain 2 / Regulator of G-protein Signalling 4; domain 2 / RGS, subdomain 2 / RGS domain superfamily / Dbl homology (DH) domain superfamily ...p115RhoGEF, RGS domain / Regulator of G protein signalling-like domain / Regulator of G protein signalling-like domain / ARHGEF1-like, PH domain / PH domain / Regulator of G-protein Signalling 4, domain 2 / Regulator of G-protein Signalling 4; domain 2 / RGS, subdomain 2 / RGS domain superfamily / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Rho guanine nucleotide exchange factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSprang, S.R. / Chen, Z.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Structure of the rgRGS domain of p115RhoGEF.
Authors: Chen, Z. / Wells, C.D. / Sternweis, P.C. / Sprang, S.R.
History
DepositionMar 22, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GUANINE NUCLEOTIDE EXCHANGE FACTOR P115RHOGEF


Theoretical massNumber of molelcules
Total (without water)24,2771
Polymers24,2771
Non-polymers00
Water1,63991
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.859, 37.432, 128.171
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GUANINE NUCLEOTIDE EXCHANGE FACTOR P115RHOGEF


Mass: 24276.924 Da / Num. of mol.: 1 / Fragment: N-TERMINAL RGS DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PTRCC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q92888
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.73 Å3/Da / Density % sol: 28.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: PEG 3350, ammonium formate, CHES, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion / PH range low: 9.6 / PH range high: 9.3
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
118-22 %(w/v)PEG33501reservoir
283 mMCHES1reservoir
380-240 mMammonium formate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.9→16 Å / Num. all: 14781 / Num. obs: 13303 / % possible obs: 90 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.12 / Rsym value: 0.12 / Net I/σ(I): 12.1
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 4.8 / Num. unique all: 1152 / Rsym value: 0.485 / % possible all: 79.6
Reflection shell
*PLUS
% possible obs: 79.6 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SE-MET STRUCTURE OF THE SAME PROTEIN SOLVED BY MAD PHASING FROM A FOUR-WAVELENGTH MAD DATASET COLLECTED AT CHESS F2 BEAMLINE (UNPUBLISHED DATA)

Resolution: 1.9→15.55 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1423020.44 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1352 10.3 %RANDOM
Rwork0.219 ---
all0.24 14639 --
obs0.219 13175 90 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.57 Å2 / ksol: 0.364 e/Å3
Displacement parametersBiso mean: 33 Å2
Baniso -1Baniso -2Baniso -3
1-11.72 Å20 Å20 Å2
2---3.48 Å20 Å2
3----8.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 1.9→15.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1534 0 0 91 1625
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d20
X-RAY DIFFRACTIONc_improper_angle_d0.98
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.339 181 9.4 %
Rwork0.304 1754 -
obs-1965 81.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10.3 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 33 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.98
LS refinement shell
*PLUS
Rfactor Rfree: 0.339 / % reflection Rfree: 9.4 % / Rfactor Rwork: 0.304

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