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- PDB-1kmt: Crystal structure of RhoGDI Glu(154,155)Ala mutant -

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Basic information

Entry
Database: PDB / ID: 1kmt
TitleCrystal structure of RhoGDI Glu(154,155)Ala mutant
ComponentsRho GDP-dissociation inhibitor 1
KeywordsPROTEIN BINDING / IMMUNOGLOBULIN FOLD / BETA SANDWICH MOTIF / ISOPRENYL-BINDING
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 / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsMateja, A. / Devedjiev, Y. / Krowarsh, D. / Longenecker, K. / Dauter, Z. / Otlewski, J. / Derewenda, Z.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2002
Title: The impact of Glu-->Ala and Glu-->Asp mutations on the crystallization properties of RhoGDI: the structure of RhoGDI at 1.3 A resolution.
Authors: Mateja, A. / Devedjiev, Y. / Krowarsch, D. / Longenecker, K. / Dauter, Z. / Otlewski, J. / Derewenda, Z.S.
History
DepositionDec 17, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 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)31,9632
Polymers31,9632
Non-polymers00
Water10,665592
1
A: Rho GDP-dissociation inhibitor 1


Theoretical massNumber of molelcules
Total (without water)15,9811
Polymers15,9811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Rho GDP-dissociation inhibitor 1


Theoretical massNumber of molelcules
Total (without water)15,9811
Polymers15,9811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.099, 35.921, 67.506
Angle α, β, γ (deg.)79.19, 82.66, 76.42
Int Tables number1
Space group name H-MP1
DetailsThe biologically relevant portion is thought to be a monomer

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Components

#1: Protein Rho GDP-dissociation inhibitor 1 / Rho GDI 1 / Rho-GDI alpha


Mass: 15981.298 Da / Num. of mol.: 2 / Mutation: E154A, E155A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P52565
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 592 / 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: 2.46 Å3/Da / Density % sol: 49.99 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 8.5
Details: PEG 4000, Tris-HCl, Lithium sulfate, methylpentane diol, pH 8.5, VAPOR DIFFUSION, temperature 294K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
124 %PEG40001reservoir
2100 mMTris1reservoirpH8.5
3200 mM1reservoirLiSO4
42.5 %MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 21, 2001
RadiationMonochromator: monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.25→25 Å / Num. all: 75214 / Num. obs: 75214 / % possible obs: 89 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2 % / Rsym value: 0.021 / Net I/σ(I): 18.6
Reflection shellResolution: 1.25→1.29 Å / Num. unique all: 4629 / Rsym value: 0.143 / % possible all: 55
Reflection
*PLUS
% possible obs: 89 % / Num. measured all: 147519 / Rmerge(I) obs: 0.021
Reflection shell
*PLUS
% possible obs: 55 % / Rmerge(I) obs: 0.143 / Mean I/σ(I) obs: 3.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→25 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.957 / SU B: 4.457 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.056 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19532 3451 4.9 %RANDOM
Rwork0.15778 ---
obs0.15962 66305 93.04 %-
all-69756 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.846 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20.01 Å2-0.01 Å2
2---0.02 Å2-0.01 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4396 0 0 592 4988
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222246
X-RAY DIFFRACTIONr_bond_other_d00.022046
X-RAY DIFFRACTIONr_angle_refined_deg2.2121.9593036
X-RAY DIFFRACTIONr_angle_other_deg0.87534770
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0813274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.02715420
X-RAY DIFFRACTIONr_chiral_restr0.0980.2334
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022450
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02462
X-RAY DIFFRACTIONr_nbd_refined0.3160.3406
X-RAY DIFFRACTIONr_nbd_other0.2280.31910
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.240.5801
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2420.39
X-RAY DIFFRACTIONr_symmetry_vdw_other0.220.329
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3190.559
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it2.57921370
X-RAY DIFFRACTIONr_mcangle_it3.6432218
X-RAY DIFFRACTIONr_scbond_it3.4052876
X-RAY DIFFRACTIONr_scangle_it4.9473818
X-RAY DIFFRACTIONr_rigid_bond_restr1.57822246
X-RAY DIFFRACTIONr_sphericity_free2.2812622
X-RAY DIFFRACTIONr_sphericity_bonded3.39622196
LS refinement shellHighest resolution: 1.3 Å / Rfactor Rfree: 0.204 / Rfactor Rwork: 0.188 / Total num. of bins used: 20
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.195 / Rfactor Rwork: 0.158
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.006
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.2

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