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- PDB-3cpi: Crystal structure of yeast Rab-GDI -

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Basic information

Entry
Database: PDB / ID: 3cpi
TitleCrystal structure of yeast Rab-GDI
ComponentsRab GDP-dissociation inhibitor
KeywordsPROTEIN TRANSPORT / Rab / GDI / vesicular transport / Cytoplasm / GTPase activation / Phosphoprotein
Function / homology
Function and homology information


Rab GDP-dissociation inhibitor activity / RAB GEFs exchange GTP for GDP on RABs / small GTPase-mediated signal transduction / vesicle-mediated transport / Neutrophil degranulation / GTPase activator activity / protein transport / 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
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKravchenko, S. / Ignatev, A. / Goody, R.S. / Rak, A. / Pylypenko, O.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: A structural model of the GDP dissociation inhibitor rab membrane extraction mechanism.
Authors: Ignatev, A. / Kravchenko, S. / Rak, A. / Goody, R.S. / Pylypenko, O.
History
DepositionMar 31, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 6, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
G: Rab GDP-dissociation inhibitor
H: Rab GDP-dissociation inhibitor


Theoretical massNumber of molelcules
Total (without water)102,5422
Polymers102,5422
Non-polymers00
Water14,358797
1
G: Rab GDP-dissociation inhibitor


Theoretical massNumber of molelcules
Total (without water)51,2711
Polymers51,2711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
H: Rab GDP-dissociation inhibitor


Theoretical massNumber of molelcules
Total (without water)51,2711
Polymers51,2711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.460, 159.780, 77.093
Angle α, β, γ (deg.)90.00, 90.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Rab GDP-dissociation inhibitor / Rab GDI / Secretory pathway GDP dissociation inhibitor / yeast Rab-GDI


Mass: 51271.230 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pET19 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P39958
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 797 / 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: 3.39 Å3/Da / Density % sol: 63.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→19.97 Å / Num. all: 60538 / Num. obs: 59630 / % possible obs: 98.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 2.3→2.35 Å / % possible all: 80

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345data collection
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ukv, chain G

1ukv


Resolution: 2.3→19.97 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.918 / SU B: 6.195 / SU ML: 0.153 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.254 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2426 2982 5 %RANDOM
Rwork0.19688 ---
all0.2 60538 --
obs0.1992 56646 100 %-
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: 38.073 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20 Å2-0.07 Å2
2---0.41 Å20 Å2
3---0.89 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6979 0 0 797 7776
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0227139
X-RAY DIFFRACTIONr_angle_refined_deg1.0581.9739653
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4195874
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.56224.528318
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.863151279
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9211530
X-RAY DIFFRACTIONr_chiral_restr0.0730.21060
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025352
X-RAY DIFFRACTIONr_nbd_refined0.1870.23267
X-RAY DIFFRACTIONr_nbtor_refined0.3020.24846
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2685
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1130.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.216
X-RAY DIFFRACTIONr_mcbond_it0.5331.54485
X-RAY DIFFRACTIONr_mcangle_it0.95427065
X-RAY DIFFRACTIONr_scbond_it1.13633012
X-RAY DIFFRACTIONr_scangle_it1.8664.52588
LS refinement shellResolution: 2.301→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 189 -
Rwork0.24 3583 -
obs--100 %

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