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- PDB-1gnd: GUANINE NUCLEOTIDE DISSOCIATION INHIBITOR, ALPHA-ISOFORM -

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Basic information

Entry
Database: PDB / ID: 1gnd
TitleGUANINE NUCLEOTIDE DISSOCIATION INHIBITOR, ALPHA-ISOFORM
ComponentsGUANINE NUCLEOTIDE DISSOCIATION INHIBITOR
KeywordsGTPASE ACTIVATION
Function / homology
Function and homology information


RAB GEFs exchange GTP for GDP on RABs / Rab GDP-dissociation inhibitor activity / negative regulation of protein targeting to membrane / Rab protein signal transduction / negative regulation of axonogenesis / vesicle-mediated transport / GTPase activator activity / protein transport / Golgi apparatus / cytosol / cytoplasm
Similarity search - Function
Rab GDI protein / Guanine Nucleotide Dissociation Inhibitor; domain 2 / Guanine Nucleotide Dissociation Inhibitor, domain 2 / GDP dissociation inhibitor / GDP dissociation inhibitor / Guanine Nucleotide Dissociation Inhibitor, domain 1 / Guanine Nucleotide Dissociation Inhibitor; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich ...Rab GDI protein / Guanine Nucleotide Dissociation Inhibitor; domain 2 / Guanine Nucleotide Dissociation Inhibitor, domain 2 / GDP dissociation inhibitor / GDP dissociation inhibitor / Guanine Nucleotide Dissociation Inhibitor, domain 1 / Guanine Nucleotide Dissociation Inhibitor; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Rab GDP dissociation inhibitor alpha
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.81 Å
AuthorsSchalk, I. / Zeng, K. / Wu, S.-K. / Stura, E.A. / Metteson, J. / Huang, M. / Tandon, A. / Wilson, I.A. / Balch, W.E.
Citation
Journal: Nature / Year: 1996
Title: Structure and mutational analysis of Rab GDP-dissociation inhibitor.
Authors: Schalk, I. / Zeng, K. / Wu, S.K. / Stura, E.A. / Matteson, J. / Huang, M. / Tandon, A. / Wilson, I.A. / Balch, W.E.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Crystallization and Preliminary Crystallographic Data for Rab Guanine Nucleotide Dissociation Inhibitor (Rabgdi) from Bovine Brain
Authors: Schalk, I.J. / Stura, E.A. / Matteson, J. / Wilson, I.A. / Balch, W.E.
History
DepositionJul 10, 1996Processing site: BNL
Revision 1.0Feb 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GUANINE NUCLEOTIDE DISSOCIATION INHIBITOR


Theoretical massNumber of molelcules
Total (without water)50,6201
Polymers50,6201
Non-polymers00
Water7,530418
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.800, 43.500, 63.200
Angle α, β, γ (deg.)90.00, 104.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein GUANINE NUCLEOTIDE DISSOCIATION INHIBITOR


Mass: 50620.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ALPHA-ISOFORM / Source: (gene. exp.) Bos taurus (cattle) / Tissue: BRAIN / Gene: BOVGDI / Plasmid: PET-11DHIS / Gene (production host): BOVGDI / Production host: Escherichia coli (E. coli) / References: UniProt: P21856
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 418 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 45 %
Crystal grow
*PLUS
pH: 6.25 / Method: unknown
Components of the solutions
*PLUS
Conc.: 1.73 M / Common name: ammonium salfate

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Dec 29, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 42588 / % possible obs: 97.1 % / Redundancy: 3 % / Rmerge(I) obs: 0.1
Reflection
*PLUS
Highest resolution: 1.81 Å

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XENGENV. 2.1data reduction
X-PLOR3.1phasing
RefinementResolution: 1.81→6 Å / σ(F): 2
RfactorNum. reflection
Rfree0.275 -
Rwork0.198 -
obs0.198 33282
Displacement parametersBiso mean: 28.2 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.81→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3406 0 418 0 3824
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.66
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Num. reflection all: 40982 / Rfactor all: 0.211
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_deg25.2
X-RAY DIFFRACTIONx_improper_angle_deg1.42

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