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- PDB-2bxw: CRYSTAL STRUCTURE OF RHOGDI Lys(135,138,141)Tyr MUTANT -

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Basic information

Entry
Database: PDB / ID: 2bxw
TitleCRYSTAL STRUCTURE OF RHOGDI Lys(135,138,141)Tyr MUTANT
ComponentsRHO GDP-DISSOCIATION INHIBITOR 1
KeywordsINHIBITOR / CRYSTAL ENGINEERING / RATIONAL SURFACE MUTAGENESIS / GTPASE ACTIVATION
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
FORMIC ACID / Rho GDP-dissociation inhibitor 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSikorska, M. / Cooper, D.R. / Otlewski, J. / Derewenda, Z.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: Protein Crystallization by Surface Entropy Reduction: Optimization of the Ser Strategy
Authors: Cooper, D.R. / Boczek, T. / Grelewska, K. / Pinkowska, M. / Sikorska, M. / Zawadzki, M. / Derewenda, Z.S.
History
DepositionJul 27, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 30, 2012Group: Other
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)32,6135
Polymers32,3992
Non-polymers2143
Water3,837213
1
A: RHO GDP-DISSOCIATION INHIBITOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4144
Polymers16,1991
Non-polymers2143
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RHO GDP-DISSOCIATION INHIBITOR 1


Theoretical massNumber of molelcules
Total (without water)16,1991
Polymers16,1991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.308, 77.308, 171.659
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein RHO GDP-DISSOCIATION INHIBITOR 1 / RHO GDI 1 / RHO-GDI ALPHA


Mass: 16199.353 Da / Num. of mol.: 2 / Fragment: ISOPRENYL-BINDING DOMAIN, RESIDUES 67-204 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: RHOGDIY135, 138, 141Y / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P52565
#2: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LYS 135 TO TYR ENGINEERED RESIDUE IN CHAIN A, LYS 138 TO TYR ...ENGINEERED RESIDUE IN CHAIN A, LYS 135 TO TYR ENGINEERED RESIDUE IN CHAIN A, LYS 138 TO TYR ENGINEERED RESIDUE IN CHAIN A, LYS 141 TO TYR ENGINEERED RESIDUE IN CHAIN B, LYS 135 TO TYR ENGINEERED RESIDUE IN CHAIN B, LYS 138 TO TYR ENGINEERED RESIDUE IN CHAIN B, LYS 141 TO TYR REGULATES THE GDP/GTP EXCHANGE REACTION OF THE RHO PROTEINS BY INHIBITING THE DISSOCIATION OF GDP FROM THEM, AND THE SUBSEQUENT BINDING OF GTP TO THEM.
Sequence detailsN-TERMINAL RESIDUES WERE CLONING ARTIFACTS. LYSINE MUTATIONS TO PROMOTE CRYSTALLIZATION.

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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: 4.29 Å3/Da / Density % sol: 71 %
Crystal growpH: 7.88 / Details: 4M NA FORMATE, pH 7.88

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 3, 2005 / Details: OSMIC MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 23248 / % possible obs: 97.1 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 26.1
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 6.44 / % possible all: 80.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KMT

1kmt


Resolution: 2.4→66.96 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.928 / SU B: 9.182 / SU ML: 0.118 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.196 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1056 4.6 %RANDOM
Rwork0.178 ---
obs0.18 22152 97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.12 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å20.54 Å20 Å2
2--1.08 Å20 Å2
3----1.61 Å2
Refinement stepCycle: LAST / Resolution: 2.4→66.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2238 0 14 213 2465
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222305
X-RAY DIFFRACTIONr_bond_other_d0.0010.022063
X-RAY DIFFRACTIONr_angle_refined_deg2.2641.9663117
X-RAY DIFFRACTIONr_angle_other_deg1.40234795
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0615274
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.39223.462104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.87215400
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9561514
X-RAY DIFFRACTIONr_chiral_restr0.0950.2335
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022514
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02486
X-RAY DIFFRACTIONr_nbd_refined0.170.2305
X-RAY DIFFRACTIONr_nbd_other0.1520.21972
X-RAY DIFFRACTIONr_nbtor_refined0.1690.21052
X-RAY DIFFRACTIONr_nbtor_other0.0780.21421
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2172
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.110.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1540.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.220.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7531.51787
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.80522230
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.26331144
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.744.5887
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.336 54
Rwork0.22 1317
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2257-0.6363-0.14873.24441.72541.3476-0.0019-0.03330.02210.0394-0.09570.08950.007-0.10340.0975-0.11420.00920.0189-0.0975-0.00740.063624.0317.52825.031
20.30290.27440.26764.41772.30891.45030.0030.0075-0.0383-0.0053-0.07050.0944-0.0251-0.0750.0675-0.1292-0.01310.0153-0.1018-0.00490.031526.154-13.0690.891
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A65 - 202
2X-RAY DIFFRACTION2B65 - 202

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