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- PDB-1eq6: 1.9 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF THE SACCHAROMYCES CE... -

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Basic information

Entry
Database: PDB / ID: 1eq6
Title1.9 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF THE SACCHAROMYCES CEREVISIAE RAN-BINDING PROTEIN MOG1P
ComponentsMOG1P
KeywordsPROTEIN TRANSPORT / alpha-beta
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 / MAD PLUS SIR / Resolution: 1.9 Å
AuthorsStewart, M. / Baker, R.P.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: 1.9 A resolution crystal structure of the Saccharomyces cerevisiae Ran-binding protein Mog1p.
Authors: Stewart, M. / Baker, R.P.
History
DepositionApr 3, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
A: MOG1P


Theoretical massNumber of molelcules
Total (without water)21,1611
Polymers21,1611
Non-polymers00
Water2,234124
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.672, 51.963, 112.234
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein MOG1P


Mass: 21160.680 Da / Num. of mol.: 1 / Fragment: RESIDUES 30-218
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: PMW172 / Production host: Escherichia coli (E. coli) / References: UniProt: P47123
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.73 Å3/Da / Density % sol: 48.5 % / Description: 3A PHASES OBTAINED FROM SE-MET MAD PLUS Hg SIR
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG4000, glycerol, sodium acetate, DTT, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 18K
Crystal
*PLUS
Density % sol: 49.5 %
Crystal grow
*PLUS
Temperature: 291 K / pH: 5.6 / Method: vapor diffusion
Details: Baker, R.P.,(2000) Acta Crystallog. Sect., D56, 229.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.2 Mammonium acetate1reservoir
21 Msodium citrate1reservoir
330 %PEG40001reservoir
410-12 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID2 / Wavelength: 0.9887
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9887 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 18951 / Num. obs: 18625 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 11.5
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 4.9 / Num. unique all: 2679 / Rsym value: 0.146 / % possible all: 98.5
Reflection shell
*PLUS
% possible obs: 98.7 % / Rmerge(I) obs: 0.146

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Processing

Software
NameVersionClassification
SHARPphasing
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD PLUS SIR / Resolution: 1.9→20 Å / Cross valid method: FREE-R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER / Details: used maximum likelihood target "mlf"
RfactorNum. reflection% reflectionSelection details
Rfree0.2458 944 5 %RANDOM
Rwork0.2171 ---
all0.2185 18951 --
obs0.2185 18625 98.3 %-
Displacement parametersBiso mean: 33.32 Å2
Baniso -1Baniso -2Baniso -3
1-1.629 Å20 Å20 Å2
2---12.176 Å20 Å2
3---10.547 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.23 Å
Luzzati d res low-20 Å
Luzzati sigma a0.12 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1488 0 0 124 1612
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.57
X-RAY DIFFRACTIONc_dihedral_angle_d25.32
X-RAY DIFFRACTIONc_improper_angle_d0.923
X-RAY DIFFRACTIONc_mcbond_it1.55
X-RAY DIFFRACTIONc_mcangle_it2.2
X-RAY DIFFRACTIONc_scbond_it2.49
X-RAY DIFFRACTIONc_scangle_it3.35
LS refinement shellResolution: 1.9→1.97 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.268 101 5.5 %
Rwork0.227 1715 -
obs--98.5 %
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.32
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.923
LS refinement shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 1.97 Å / Rfactor Rfree: 0.268 / % reflection Rfree: 5.5 % / Rfactor Rwork: 0.227 / Rfactor obs: 0.227

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