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- PDB-1jhs: Protein Mog1 E65A mutant -

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Basic information

Entry
Database: PDB / ID: 1jhs
TitleProtein Mog1 E65A mutant
ComponentsMOG1 PROTEIN
KeywordsGENE REGULATION / NUCLEAR-PROTEIN IMPORT / GSP1
Function / homology
Function and homology information


mRNA transport / guanyl-nucleotide exchange factor activity / small GTPase binding / protein import into nucleus / nucleus
Similarity search - Function
Ran-interacting Mog1 protein / Ran-interacting Mog1 protein / Mog1/PsbP, alpha/beta/alpha sandwich / Protein Transport Mog1p; Chain A / Mog1/PsbP, alpha/beta/alpha sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Nuclear import protein MOG1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBaker, R.P. / Harreman, M.T. / Ecclestone, J.F. / Corbett, A.H. / Stewart, M.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Interaction between Ran and Mog1 is required for efficient nuclear protein import
Authors: Baker, R.P. / Harreman, M.T. / Ecclestone, J.F. / Corbett, A.H. / Stewart, M.
History
DepositionJun 28, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MOG1 PROTEIN


Theoretical massNumber of molelcules
Total (without water)21,0161
Polymers21,0161
Non-polymers00
Water3,531196
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.365, 48.972, 111.976
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein MOG1 PROTEIN / Mog1p / nuclear protein that interacts with GTP-Gsp1p / hypothetical protein YJR074w


Mass: 21015.564 Da / Num. of mol.: 1 / Mutation: E65A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: Mog1 / Production host: Escherichia coli (E. coli) / Strain (production host): pET / References: UniProt: P47123
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.63 Å3/Da / Density % sol: 53.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG, VAPOR DIFFUSION, HANGING DROP at 291K
Crystal grow
*PLUS
Temperature: 291 K / pH: 5.6 / Method: vapor diffusion, hanging drop / Details: Baker, R.P., (2000) Acta Crystallogr., D56, 229.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
116-20 %PEG40001reservoir
220 %glycerol1reservoir
310 mMdithiothreitol1reservoir
50.1-0.25 %beta-octylglucoside1reservoir
610-12 mg/mlprotein1drop
70.2 Mammonium acetate1drop
81 Msodium citrate1droppH5.6
930 %PEG40001drop
4acetate1reservoiror MES, pH6.0-6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 24, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.9→31.2 Å / Num. all: 18211 / Num. obs: 18191 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 6.4
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.076 / Mean I/σ(I) obs: 8.9 / % possible all: 99.9
Reflection
*PLUS
Num. measured all: 62794
Reflection shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 2 Å / % possible obs: 99.9 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Mog1 native

Resolution: 1.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.248 920 5 %random
Rwork0.208 ---
all-18211 --
obs-18191 99.9 %-
Displacement parametersBiso mean: 18.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.812 Å20 Å20 Å2
2---2.361 Å20 Å2
3---4.173 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å / Luzzati sigma a obs: 0.06 Å
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1478 0 0 196 1674
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_d1.46
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 31.2 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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