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- PDB-1lv0: Crystal structure of the Rab effector guanine nucleotide dissocia... -

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Basic information

Entry
Database: PDB / ID: 1lv0
TitleCrystal structure of the Rab effector guanine nucleotide dissociation inhibitor (GDI) in complex with a geranylgeranyl (GG) peptide
ComponentsRAB GDP disossociation inhibitor alpha
KeywordsSIGNALING PROTEIN / Protein-ligand complex
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
GERAN-8-YL GERAN / Rab GDP dissociation inhibitor alpha
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAn, Y. / Shao, Y. / Alory, C. / Matteson, J. / Sakisaka, T. / Chen, W. / Gibbs, R.A. / Wilson, I.A. / Balch, W.E.
CitationJournal: Structure / Year: 2003
Title: Geranylgeranyl switching regulates GDI-Rab GTPase recycling.
Authors: An, Y. / Shao, Y. / Alory, C. / Matteson, J. / Sakisaka, T. / Chen, W. / Gibbs, R.A. / Wilson, I.A. / Balch, W.E.
History
DepositionMay 23, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RAB GDP disossociation inhibitor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4595
Polymers50,8971
Non-polymers5634
Water6,630368
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.230, 42.861, 89.104
Angle α, β, γ (deg.)90.00, 103.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RAB GDP disossociation inhibitor alpha / RAB GDI ALPHA / GDI-1 / SMG P25A GDI


Mass: 50896.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Plasmid: PET-11DHIS / Production host: Escherichia coli (E. coli) / References: UniProt: P21856
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GER / GERAN-8-YL GERAN


Mass: 274.484 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H34
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 368 / 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: 2.27 Å3/Da / Density % sol: 45.79 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: Ammonium Sulfate, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Crystal grow
*PLUS
Temperature: 22.5 ℃ / pH: 6.25 / Method: vapor diffusion, sitting drop
Details: Luan, P., (2000) Traffic, 1, 270., Schalk, I., (1996) Nature,381, 42.
Components of the solutions
*PLUS
Conc.: 1.73 M / Common name: ammonium sulfate

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Data collection

DiffractionMean temperature: 98 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.033 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 12, 2000
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 30213 / Num. obs: 30213 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 12.7 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 12.7
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 0.419 / Mean I/σ(I) obs: 1.4 / Num. unique all: 1325 / Rsym value: 0.419 / % possible all: 85.9
Reflection
*PLUS
Num. measured all: 68840
Reflection shell
*PLUS
% possible obs: 85.9 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
CNS0.9refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1D5T

1d5t


Resolution: 2→19.96 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.249 2905 10.1 %RANDOM
Rwork0.196 ---
all0.196 28728 --
obs0.196 28728 91.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.4971 Å2 / ksol: 0.342343 e/Å3
Displacement parametersBiso mean: 29.2 Å2
Baniso -1Baniso -2Baniso -3
1-3.74 Å20 Å24.3 Å2
2---4.51 Å20 Å2
3---0.77 Å2
Refine analyzeLuzzati coordinate error free: 0.3 Å / Luzzati sigma a free: 0.32 Å
Refinement stepCycle: LAST / Resolution: 2→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3431 0 35 368 3834
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_mcbond_it1.621.5
X-RAY DIFFRACTIONc_mcangle_it2.392
X-RAY DIFFRACTIONc_scbond_it2.612
X-RAY DIFFRACTIONc_scangle_it3.832.5
LS refinement shellResolution: 2→2.03 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 140 10.4 %
Rwork0.301 1211 -
obs--86.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3GG_PAR.TXTGG_TOP.TXT
X-RAY DIFFRACTION4ION.PARAMION.TOP
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0055
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.7

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