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- PDB-4xri: Crystal Structure of Importin Beta in an Ammonium Sulfate Condition -

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Basic information

Entry
Database: PDB / ID: 4xri
TitleCrystal Structure of Importin Beta in an Ammonium Sulfate Condition
ComponentsPutative uncharacterized protein
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 / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe ...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 / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 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 2.0Mar 14, 2018Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Derived calculations
Category: atom_site / diffrn_source ...atom_site / diffrn_source / pdbx_audit_support / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization / _struct_site_gen.auth_seq_id
Revision 2.1Jan 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: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,32619
Polymers96,6331
Non-polymers1,69318
Water5,621312
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-99 kcal/mol
Surface area39470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.860, 85.040, 207.750
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative uncharacterized protein


Mass: 96632.828 Da / Num. of mol.: 1 / Mutation: S107P; V143A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
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
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 2.92 Å3/Da / Density % sol: 57.94 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 1 M ammonium sulfate, 5 mM magnesium chloride, 100 mM sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.82661 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82661 Å / Relative weight: 1
ReflectionResolution: 2.05→37.33 Å / Num. obs: 70347 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 47.36 Å2 / Rmerge F obs: 1 / Rmerge(I) obs: 0.032 / Rrim(I) all: 0.038 / Χ2: 1.025 / Net I/σ(I): 19 / Num. measured all: 254741
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
2.05-2.173.70.7580.6442.044197211306112720.75599.7
2.17-2.30.90.3573.5132194900489290.4299.2
2.3-2.550.9710.1846.574849413137131000.21699.7
2.55-3.350.9980.05318.77500920650205270.06399.4
3.35-3.750.9990.02637.5816382472446520.0398.5
3.75-4.150.9990.02146.0910561308730450.02598.6
4.15-4.550.9990.01851.997446212220880.02198.4
4.55-140.9990.01657.2621897659964720.01998.1
14-1710.0176.333921221200.01198.4
17-5010.01261.013941591420.01589.3
5012

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASER2.5.5phasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ND2

3nd2


Resolution: 2.05→37.332 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.227 3556 5.06 %
Rwork0.1983 66689 -
obs0.1997 70245 99.2 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126 Å2 / Biso mean: 54.9612 Å2 / Biso min: 25.52 Å2
Refinement stepCycle: final / Resolution: 2.05→37.332 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6653 0 99 312 7064
Biso mean--72.14 53.74 -
Num. residues----865
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036846
X-RAY DIFFRACTIONf_angle_d0.7469282
X-RAY DIFFRACTIONf_chiral_restr0.0261054
X-RAY DIFFRACTIONf_plane_restr0.0041217
X-RAY DIFFRACTIONf_dihedral_angle_d13.732500
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.07810.37341810.330126332814100
2.0781-2.10780.3751390.318526272766100
2.1078-2.13920.37161490.293526212770100
2.1392-2.17270.32421340.288126732807100
2.1727-2.20830.31441380.27692606274499
2.2083-2.24640.31681410.26792684282599
2.2464-2.28720.28791360.25882580271699
2.2872-2.33120.30561400.251526652805100
2.3312-2.37880.27521380.23826322770100
2.3788-2.43050.28961410.235826922833100
2.4305-2.4870.25861410.227426342775100
2.487-2.54920.25291370.2326532790100
2.5492-2.61810.26331420.22426922834100
2.6181-2.69510.27581390.22312627276699
2.6951-2.78210.27971400.21762654279499
2.7821-2.88150.22471420.216126752817100
2.8815-2.99680.24121400.218426852825100
2.9968-3.13310.24441400.221526782818100
3.1331-3.29820.26221430.2112693283699
3.2982-3.50470.2261410.19722663280499
3.5047-3.77510.23511390.17512650278998
3.7751-4.15450.16951410.16972683282499
4.1545-4.75470.17371400.15882714285498
4.7547-5.98640.2211420.19322704284698
5.9864-37.33840.1781520.16862871302398

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