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- PDB-5h1d: Crystal structure of C-terminal of RhoGDI2 -

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Basic information

Entry
Database: PDB / ID: 5h1d
TitleCrystal structure of C-terminal of RhoGDI2
ComponentsRho GDP-dissociation inhibitor 2
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


cellular response to redox state / Rho GDP-dissociation inhibitor activity / negative regulation of trophoblast cell migration / regulation of Rho protein signal transduction / CDC42 GTPase cycle / RHOH GTPase cycle / Rho protein signal transduction / RHOG GTPase cycle / RHOA GTPase cycle / RAC3 GTPase cycle ...cellular response to redox state / Rho GDP-dissociation inhibitor activity / negative regulation of trophoblast cell migration / regulation of Rho protein signal transduction / CDC42 GTPase cycle / RHOH GTPase cycle / Rho protein signal transduction / RHOG GTPase cycle / RHOA GTPase cycle / RAC3 GTPase cycle / RAC1 GTPase cycle / GTPase activator activity / small GTPase binding / cytoplasmic vesicle / cytoskeleton / GTPase activity / extracellular exosome / membrane / cytoplasm / cytosol
Similarity search - Function
Coagulation Factor XIII, subunit A, domain 1 / Rho protein GDP-dissociation inhibitor / Rho GDP-dissociation inhibitor domain superfamily / RHO protein GDP dissociation inhibitor / Coagulation Factor XIII; Chain A, domain 1 / Distorted Sandwich / Immunoglobulin E-set / Mainly Beta
Similarity search - Domain/homology
Rho GDP-dissociation inhibitor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.494 Å
AuthorsLiu, J.
CitationJournal: Biochim. Biophys. Acta / Year: 2017
Title: NMR characterization of weak interactions between RhoGDI2 and fragment screening hits.
Authors: Liu, J. / Gao, J. / Li, F. / Ma, R. / Wei, Q. / Wang, A. / Wu, J. / Ruan, K.
History
DepositionOct 8, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2017Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rho GDP-dissociation inhibitor 2


Theoretical massNumber of molelcules
Total (without water)16,4281
Polymers16,4281
Non-polymers00
Water3,621201
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.020, 55.020, 96.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-432-

HOH

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Components

#1: Protein Rho GDP-dissociation inhibitor 2 / Rho GDI 2 / Ly-GDI / Rho-GDI beta


Mass: 16427.709 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 61-201
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARHGDIB, GDIA2, GDID4, RAP1GN1
Production host: Escherichia coli BL21-Gold(DE3)pLysS AG (bacteria)
References: UniProt: P52566
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.36 Å3/Da / Density % sol: 47.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 30% PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.494→47.833 Å / Num. obs: 24846 / % possible obs: 99.9 % / Redundancy: 13.6 % / Biso Wilson estimate: 16.66 Å2 / Rsym value: 0.09 / Net I/av σ(I): 4.389 / Net I/σ(I): 18.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.494-1.5713.80.5021.31100
1.57-1.67140.3182.21100
1.67-1.79140.1973.51100
1.79-1.93140.1255.41100
1.93-2.1113.90.09171100
2.11-2.3613.80.0798.31100
2.36-2.7313.50.0867.11100
2.73-3.3413.10.0995.71100
3.34-4.7211.80.0688.7199.9
4.72-36.3410.70.05111.7195.5

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Processing

Software
NameVersionClassification
SCALA3.3.21data scaling
PHENIX1.10_2155refinement
PDB_EXTRACT3.2data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RHO

1rho


Resolution: 1.494→36.34 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 17.66
RfactorNum. reflection% reflection
Rfree0.2039 1260 5.08 %
Rwork0.1539 --
obs0.1564 24783 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 74.98 Å2 / Biso mean: 26.8029 Å2 / Biso min: 9.87 Å2
Refinement stepCycle: final / Resolution: 1.494→36.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1092 0 0 201 1293
Biso mean---42.28 -
Num. residues----135
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041119
X-RAY DIFFRACTIONf_angle_d0.7091514
X-RAY DIFFRACTIONf_chiral_restr0.076166
X-RAY DIFFRACTIONf_plane_restr0.005190
X-RAY DIFFRACTIONf_dihedral_angle_d18.179418
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.494-1.55380.20571390.14225482687100
1.5538-1.62450.22351360.130325722708100
1.6245-1.71020.18151400.128925742714100
1.7102-1.81730.1711330.124525632696100
1.8173-1.95760.21011390.137126132752100
1.9576-2.15460.2061350.138725882723100
2.1546-2.46630.21911530.15826202773100
2.4663-3.10710.21111500.179126672817100
3.1071-36.3510.1961350.16042778291398

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