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- PDB-4xrk: Crystal Structure of Importin Beta in a Polyethylene Glycol Condition -

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Basic information

Entry
Database: PDB / ID: 4xrk
TitleCrystal Structure of Importin Beta in a Polyethylene Glycol Condition
ComponentsImportin Beta
KeywordsTRANSPORT PROTEIN / Nuclear Transport / Transport Receptor / Importin-Beta Superfamily / HEAT Repeat Protein / Nuclear Import of Various Proteinaceous Cargo Molecules / Highly Flexible Proteins
Function / homology
Function and homology information


small GTPase binding / protein import into nucleus / nucleus / cytoplasm
Similarity search - Function
Importin beta family / HEAT-like repeat / Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta, N-terminal domain / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Importin N-terminal domain-containing protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.25 Å
AuthorsTauchert, M.J. / Neumann, P. / Ficner, R. / Dickmanns, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation Germany
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2016
Title: Impact of the crystallization condition on importin-beta conformation.
Authors: Tauchert, M.J. / Hemonnot, C. / Neumann, P. / Koster, S. / Ficner, R. / Dickmanns, A.
History
DepositionJan 21, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Jun 29, 2016Group: Database references
Revision 1.3Mar 14, 2018Group: Author supporting evidence / Data collection
Category: diffrn_radiation_wavelength / diffrn_source / pdbx_audit_support
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization
Revision 1.4Jan 10, 2024Group: 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
A: Importin Beta


Theoretical massNumber of molelcules
Total (without water)96,6511
Polymers96,6511
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area38860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.410, 121.190, 132.040
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein Importin Beta


Mass: 96650.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0012280 / Plasmid: pGEX-6P-3 / Details (production host): N-terminal GST-tag / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009[pREP4] / References: UniProt: G0S143

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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: 2.68 Å3/Da / Density % sol: 54.11 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.9
Details: 14 % (w/v) PEG 4000, 8 % (w/v) PEG 200, 10 mM magnesium chloride, 2 % (w/v) benzamidine hydrochloride hydrate, 100 mM Tris pH 8.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.77318 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.77318 Å / Relative weight: 1
ReflectionResolution: 3.25→44.642 Å / Num. obs: 16105 / % possible obs: 95 % / Observed criterion σ(I): -3 / Redundancy: 4.57 % / Biso Wilson estimate: 89.24 Å2 / Rmerge F obs: 0.995 / Rmerge(I) obs: 0.149 / Rrim(I) all: 0.168 / Χ2: 0.957 / Net I/σ(I): 8.02 / Num. measured all: 73621
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
3.25-3.373.660.620.7261.655559177415180.83585.6
3.37-3.670.8540.4152.9211146328930250.47992
3.67-3.870.9330.2524.665591170315620.29291.7
3.87-4.110.9120.3165.946959162715270.35593.9
4.11-4.330.9590.2597.96570121912160.28899.8
4.33-4.550.9590.2448.9754259779760.2799.9
4.55-4.770.9720.2039.844148108080.22699.8
4.77-140.9970.09213.3927158528652380.10399.1
14-170.9980.04122.543861111060.04795.5
17-500.9980.03920.044131461290.04688.4
5011

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XRI

4xri


Resolution: 3.25→44.642 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 35.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3168 803 4.99 %
Rwork0.2895 15274 -
obs0.2909 16077 95.06 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 238.76 Å2 / Biso mean: 130.2588 Å2 / Biso min: 38.98 Å2
Refinement stepCycle: final / Resolution: 3.25→44.642 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6399 0 0 0 6399
Num. residues----832
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056504
X-RAY DIFFRACTIONf_angle_d1.0248826
X-RAY DIFFRACTIONf_chiral_restr0.041012
X-RAY DIFFRACTIONf_plane_restr0.0051168
X-RAY DIFFRACTIONf_dihedral_angle_d10.262387
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2502-3.45370.41871230.35552308243188
3.4537-3.72030.35131270.31862409253692
3.7203-4.09450.35821290.30732457258693
4.0945-4.68640.31551390.281926472786100
4.6864-5.90220.34021400.29342672281299
5.9022-44.64620.26151450.26312781292698

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