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- PDB-1gdf: STRUCTURE OF RHOGDI: A C-TERMINAL BINDING DOMAIN TARGETS AN N-TER... -

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Basic information

Entry
Database: PDB / ID: 1gdf
TitleSTRUCTURE OF RHOGDI: A C-TERMINAL BINDING DOMAIN TARGETS AN N-TERMINAL INHIBITORY PEPTIDE TO GTPASES, NMR, MINIMIZED AVERAGE STRUCTURE
ComponentsRHOGDI
KeywordsRHO-GTPASE INHIBITOR / NUCLEOTIDE EXCHANGE / ISOPRENE BINDING
Function / homology
Function and homology information


Rho GDP-dissociation inhibitor activity / semaphorin-plexin signaling pathway / Rho protein signal transduction / immunological synapse / GTPase activator activity / membrane / 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 speciesBos taurus (cattle)
MethodSOLUTION NMR / HYBRID DISTANCE GEOMETRY, SIMULATED ANNEALING
AuthorsRosen, M.K. / Gosser, Y.Q.
CitationJournal: Nature / Year: 1997
Title: C-terminal binding domain of Rho GDP-dissociation inhibitor directs N-terminal inhibitory peptide to GTPases.
Authors: Gosser, Y.Q. / Nomanbhoy, T.K. / Aghazadeh, B. / Manor, D. / Combs, C. / Cerione, R.A. / Rosen, M.K.
History
DepositionMay 11, 1997Processing site: BNL
Revision 1.0Nov 19, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RHOGDI


Theoretical massNumber of molelcules
Total (without water)16,7081
Polymers16,7081
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 40NO DISTANCE VIOLATIONS 0.3 ANGSTROMS, THEN LOWEST OVERALL ENERGY
Representative

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Components

#1: Protein RHOGDI


Mass: 16708.014 Da / Num. of mol.: 1 / Fragment: ISOPRENE BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Cell line: BL21 / Plasmid: PET11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P19803

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HN(CA)CB
121CBCACONNH
131HNCO
141CCC-TOCSY-NNH
151HCC-TOCSY-NNH
16115N-TOCSY
171(H)CCH-TOCSY
181(H)CCH-COSY
19115N-NOESY
110115N/13C-NOESY

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Sample preparation

Sample conditionspH: 6.8 / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 600 MHz

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Processing

Software
NameVersionClassification
X-PLOR3model building
X-PLOR3refinement
X-PLOR3phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3BRUNGERrefinement
NMRPipestructure solution
NMRViewstructure solution
X-PLORstructure solution
RefinementMethod: HYBRID DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1
NMR ensembleConformer selection criteria: NO DISTANCE VIOLATIONS 0.3 ANGSTROMS, THEN LOWEST OVERALL ENERGY
Conformers calculated total number: 40 / Conformers submitted total number: 1

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