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- PDB-1ft0: CRYSTAL STRUCTURE OF TRUNCATED HUMAN RHOGDI K113A MUTANT -

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Basic information

Entry
Database: PDB / ID: 1ft0
TitleCRYSTAL STRUCTURE OF TRUNCATED HUMAN RHOGDI K113A MUTANT
ComponentsRHO GDP-DISSOCIATION INHIBITOR 1
KeywordsSIGNALING PROTEIN INHIBITOR / immunoglobulin fold / beta sandwich motif / isoprenyl-binding domain / GDP-dissociation inhibitor of Rho GTPases
Function / homology
Function and homology information


Rho GDP-dissociation inhibitor activity / regulation of synaptic vesicle cycle / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / regulation of Rho protein signal transduction / RHOC GTPase cycle / RHOH GTPase cycle / semaphorin-plexin signaling pathway / CDC42 GTPase cycle / Rho protein signal transduction ...Rho GDP-dissociation inhibitor activity / regulation of synaptic vesicle cycle / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / regulation of Rho protein signal transduction / RHOC GTPase cycle / RHOH GTPase cycle / semaphorin-plexin signaling pathway / CDC42 GTPase cycle / Rho protein signal transduction / immunological synapse / RHOG GTPase cycle / RHOA GTPase cycle / RAC2 GTPase cycle / RAC1 GTPase cycle / GTPase activator activity / Schaffer collateral - CA1 synapse / regulation of protein localization / cytoskeleton / negative regulation of apoptotic process / extracellular exosome / membrane / nucleus / 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 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsLongenecker, K.L. / Garrard, S.M. / Sheffield, P.J. / Derewenda, Z.S.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Protein crystallization by rational mutagenesis of surface residues: Lys to Ala mutations promote crystallization of RhoGDI.
Authors: Longenecker, K.L. / Garrard, S.M. / Sheffield, P.J. / Derewenda, Z.S.
#1: Journal: Structure / Year: 1997
Title: A modulator of rho family G proteins, rhoGDI, binds these G-proteins via an immunoglobulin-like domain and a flexible N-terminal arm
Authors: Keep, N.H. / Barnes, M. / Barsukov, I. / Badii, R. / Lian, L. / Segal, A.W. / Moody, P.C. / Roberts, G.C.
History
DepositionSep 11, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Data collection / Database references / Category: database_2 / diffrn_source / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RHO GDP-DISSOCIATION INHIBITOR 1
B: RHO GDP-DISSOCIATION INHIBITOR 1


Theoretical massNumber of molelcules
Total (without water)31,8222
Polymers31,8222
Non-polymers00
Water1,00956
1
A: RHO GDP-DISSOCIATION INHIBITOR 1


Theoretical massNumber of molelcules
Total (without water)15,9111
Polymers15,9111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RHO GDP-DISSOCIATION INHIBITOR 1


Theoretical massNumber of molelcules
Total (without water)15,9111
Polymers15,9111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-13 kcal/mol
Surface area13650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.49, 128.49, 164.34
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
DetailsThe asymmetric unit has two monomers. The biologically active species is one monomer.

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Components

#1: Protein RHO GDP-DISSOCIATION INHIBITOR 1 / GUANINE NUCLEOTIDE DISSOCIATION INHIBITOR / RHOGDI


Mass: 15911.137 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN / Mutation: K113A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEX / Production host: Escherichia coli (E. coli) / References: UniProt: P52565
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 4.1 Å3/Da / Density % sol: 70 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: ammonium sulfate, Na/K tartrate, and sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17-15 mg/mlprotein1drop
250 %satammonium sulfate1reservoir
3200 mMsodium/potassium tartrate1reservoir
4100 mMsodium citrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9091
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 6, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9091 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 15110 / Num. obs: 15110 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 69 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 16.8
Reflection shellResolution: 2.6→2.66 Å / Redundancy: 4 % / Rmerge(I) obs: 0.333 / Num. unique all: 1015 / % possible all: 94.9
Reflection
*PLUS
Num. measured all: 73487
Reflection shell
*PLUS
% possible obs: 94.9 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.7

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.6→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1001 -Random
Rwork0.226 ---
all-16245 --
obs-15073 92.8 %-
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2147 0 0 56 2203
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0074
X-RAY DIFFRACTIONc_angle_deg1.48
X-RAY DIFFRACTIONc_dihedral_angle_d26.81
X-RAY DIFFRACTIONc_improper_angle_d0.782
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.81
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.782

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