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- PDB-2z0q: Crystal structure of DH-PH domain of RhoGEF3(Xpln) -

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Basic information

Entry
Database: PDB / ID: 2z0q
TitleCrystal structure of DH-PH domain of RhoGEF3(Xpln)
ComponentsRho guanine nucleotide exchange factor 3
KeywordsSIGNALING PROTEIN / DH-PH domain / Guanine-nucleotide releasing factor / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


guanyl-nucleotide exchange factor activity => GO:0005085 / : / NRAGE signals death through JNK / G alpha (12/13) signalling events / positive regulation of Rho protein signal transduction / intracellular signal transduction / cytoplasm
Similarity search - Function
Dbl Homology Domain; Chain A / Dbl homology (DH) domain / Dbl homology (DH) domain signature. / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain superfamily / RhoGEF domain / Dbl homology (DH) domain profile. / Dbl homology (DH) domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) ...Dbl Homology Domain; Chain A / Dbl homology (DH) domain / Dbl homology (DH) domain signature. / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain superfamily / RhoGEF domain / Dbl homology (DH) domain profile. / Dbl homology (DH) domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Roll / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Rho guanine nucleotide exchange factor 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.79 Å
AuthorsMurayama, K. / Kato-Murayama, M. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Structure of the Rho-specific guanine nucleotide-exchange factor Xpln
Authors: Murayama, K. / Kato-Murayama, M. / Akasaka, R. / Terada, T. / Yokoyama, S. / Shirouzu, M.
History
DepositionMay 7, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 13, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 28, 2012Group: Database references / Structure summary
Revision 1.3Dec 12, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rho guanine nucleotide exchange factor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7355
Polymers40,3501
Non-polymers3844
Water6,485360
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.582, 62.670, 115.278
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 Rho guanine nucleotide exchange factor 3 / Xpln


Mass: 40350.344 Da / Num. of mol.: 1 / Fragment: DH-PH domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PX060725-06 / Production host: Cell free protein synthsis (unknown) / References: UniProt: Q91X46
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 360 / 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: 2.34 Å3/Da / Density % sol: 47.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEGMME5000, Ammonium sulfate, MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.97888, 0.97964, 0.9640
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 31, 2006
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978881
20.979641
30.9641
ReflectionResolution: 1.79→50 Å / Num. obs: 35822 / % possible obs: 99.4 % / Observed criterion σ(F): -3 / Redundancy: 7 % / Biso Wilson estimate: 21.4 Å2 / Rsym value: 0.059 / Net I/σ(I): 28.2
Reflection shellResolution: 1.79→1.85 Å / % possible all: 96.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.79→42.43 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1306850.09 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1777 5 %RANDOM
Rwork0.203 ---
obs0.203 35760 99 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.1147 Å2 / ksol: 0.348215 e/Å3
Displacement parametersBiso mean: 28.8 Å2
Baniso -1Baniso -2Baniso -3
1-1.06 Å20 Å20 Å2
2---2.02 Å20 Å2
3---0.96 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.79→42.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2613 0 20 360 2993
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.421.5
X-RAY DIFFRACTIONc_mcangle_it2.222
X-RAY DIFFRACTIONc_scbond_it2.312
X-RAY DIFFRACTIONc_scangle_it3.42.5
LS refinement shellResolution: 1.79→1.9 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.286 283 5 %
Rwork0.244 5398 -
obs--95.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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