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- PDB-1rho: STRUCTURE OF RHO GUANINE NUCLEOTIDE DISSOCIATION INHIBITOR -

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Basic information

Entry
Database: PDB / ID: 1rho
TitleSTRUCTURE OF RHO GUANINE NUCLEOTIDE DISSOCIATION INHIBITOR
ComponentsRHO GDP-DISSOCIATION INHIBITOR 1
KeywordsINHIBITOR / GTPASE ACTIVATION / PHOSPHORYLATION
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 / MIR WITH ANOMALOUS / Resolution: 2.5 Å
AuthorsKeep, N.H. / Moody, P.C.E. / Roberts, G.C.K.
CitationJournal: 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.Y. / Segal, A.W. / Moody, P.C. / Roberts, G.C.
History
DepositionOct 12, 1996Processing site: BNL
Revision 1.0Oct 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Refinement description
Category: diffrn_source / pdbx_database_status ...diffrn_source / pdbx_database_status / software / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.process_site ..._diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.process_site / _software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Aug 14, 2019Group: Data collection / Category: computing

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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
C: RHO GDP-DISSOCIATION INHIBITOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,72012
Polymers49,8553
Non-polymers8659
Water3,441191
1
A: RHO GDP-DISSOCIATION INHIBITOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9074
Polymers16,6181
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RHO GDP-DISSOCIATION INHIBITOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9074
Polymers16,6181
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: RHO GDP-DISSOCIATION INHIBITOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9074
Polymers16,6181
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
A: RHO GDP-DISSOCIATION INHIBITOR 1
C: RHO GDP-DISSOCIATION INHIBITOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8138
Polymers33,2372
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-74 kcal/mol
Surface area15460 Å2
MethodPISA
5
B: RHO GDP-DISSOCIATION INHIBITOR 1
hetero molecules

B: RHO GDP-DISSOCIATION INHIBITOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8138
Polymers33,2372
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Buried area2080 Å2
ΔGint-73 kcal/mol
Surface area15490 Å2
MethodPISA
6
A: RHO GDP-DISSOCIATION INHIBITOR 1
C: RHO GDP-DISSOCIATION INHIBITOR 1
hetero molecules

A: RHO GDP-DISSOCIATION INHIBITOR 1
C: RHO GDP-DISSOCIATION INHIBITOR 1
hetero molecules

A: RHO GDP-DISSOCIATION INHIBITOR 1
C: RHO GDP-DISSOCIATION INHIBITOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,44024
Polymers99,7116
Non-polymers1,72918
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area10710 Å2
ΔGint-267 kcal/mol
Surface area41780 Å2
MethodPISA
7
B: RHO GDP-DISSOCIATION INHIBITOR 1
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)101,44024
Polymers99,7116
Non-polymers1,72918
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation10_455y-1/3,x+1/3,-z+1/31
crystal symmetry operation11_565x-y+2/3,-y+4/3,-z+1/31
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Buried area10840 Å2
ΔGint-272 kcal/mol
Surface area41880 Å2
MethodPISA
8
B: RHO GDP-DISSOCIATION INHIBITOR 1
hetero molecules

B: RHO GDP-DISSOCIATION INHIBITOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8138
Polymers33,2372
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_455y-1/3,x+1/3,-z+1/31
Buried area2470 Å2
ΔGint-81 kcal/mol
Surface area15100 Å2
MethodPISA
9
A: RHO GDP-DISSOCIATION INHIBITOR 1
hetero molecules

C: RHO GDP-DISSOCIATION INHIBITOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8138
Polymers33,2372
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area2440 Å2
ΔGint-77 kcal/mol
Surface area15050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.570, 156.570, 132.590
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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


Mass: 16618.432 Da / Num. of mol.: 3 / Mutation: TRYPSIN PROTEOLYSIS AT R58
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HUMAN RHOGDI CDNA LOCUS HUMRH / Plasmid: PGEX2T
Gene (production host): HUMAN RHOGDI CDNA, LOCUS HUMRHOGDP M97579
Production host: Escherichia coli (E. coli) / References: UniProt: P52565
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 3.14 Å3/Da / Density % sol: 58 %
Crystal growpH: 8.5 / Details: 2 M NH4 SO4 0.1 M TRIS PH 8.5
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12 Mammonium sulfate1drop
20.1 MTris1drop
31 mMDTT1drop
41 mMsodium azide1drop
510 mg/mlprotain1drop
65 mMTris1drop
71 mMDTT1drop
81 mMsodium azide1drop
92 Mammonium sulfate1reservoir
100.1 MTris1reservoir
111 mMDTT1reservoir
121 mMsodium azide1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.977
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 28, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 20345 / % possible obs: 92.9 % / Observed criterion σ(I): 0 / Redundancy: 13.4 % / Biso Wilson estimate: 48.9 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 25.4
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 11 % / Rmerge(I) obs: 0.254 / Mean I/σ(I) obs: 8.7 / % possible all: 95.3
Reflection
*PLUS
Redundancy: 7.9 % / Num. measured all: 161161
Reflection shell
*PLUS
% possible obs: 95.3 %

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Processing

Software
NameVersionClassification
X-PLOR3.843refinement
X-PLOR3.843model building
SHELXrefinement
SHELXmodel building
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
X-PLOR3.843phasing
RefinementMethod to determine structure: MIR WITH ANOMALOUS / Resolution: 2.5→8 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Details: SELENOMETHIONINE DATA WAS STRONGER AND THEREFORE USED FOR REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.298 1000 5.1 %SHELLS
Rwork0.225 ---
obs0.225 19482 92.8 %-
Displacement parametersBiso mean: 23 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.29 Å
Luzzati d res low-8 Å
Luzzati sigma a0.33 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3427 0 45 191 3663
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.76
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.941.5
X-RAY DIFFRACTIONx_mcangle_it4.462
X-RAY DIFFRACTIONx_scbond_it5.042
X-RAY DIFFRACTIONx_scangle_it6.992.5
LS refinement shellResolution: 2.5→2.65 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.401 169 5.2 %
Rwork0.312 3099 -
obs--94.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2EXTRAPARA.PROEXTRATOP.PRO

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