[English] 日本語
Yorodumi
- PDB-4xrk: Crystal Structure of Importin Beta in a Polyethylene Glycol Condition -

+
Open data


ID or keywords:

Loading...

-
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 / Importin-beta N-terminal domain / Importin-beta N-terminal domain profile. / Importin-beta, N-terminal domain / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
Phasing

PhasingMethod: molecular replacement

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more