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- PDB-4tnm: Crystal structure of Arabidopsis importin-alpha3 armadillo repeat... -

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Basic information

Entry
Database: PDB / ID: 4tnm
TitleCrystal structure of Arabidopsis importin-alpha3 armadillo repeat domain
ComponentsImportin subunit alpha
KeywordsPROTEIN BINDING / armadillo repeat
Function / homology
Function and homology information


nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / defense response / host cell nucleus / nucleus / cytosol
Similarity search - Function
Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain / IBB domain profile. / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats ...Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain / IBB domain profile. / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Importin subunit alpha-3 / Importin subunit alpha-3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å
AuthorsWirthmueller, L. / Banfield, M.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BBJ00453 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BBK009176 United Kingdom
CitationJournal: Plant J. / Year: 2015
Title: Probing formation of cargo/importin-alpha transport complexes in plant cells using a pathogen effector.
Authors: Wirthmueller, L. / Roth, C. / Fabro, G. / Caillaud, M.C. / Rallapalli, G. / Asai, S. / Sklenar, J. / Jones, A.M. / Wiermer, M. / Jones, J.D. / Banfield, M.J.
History
DepositionJun 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Jan 14, 2015Group: Database references
Revision 1.3Feb 4, 2015Group: Derived calculations / Other
Revision 1.4Sep 20, 2017Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_keywords
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.5Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Importin subunit alpha


Theoretical massNumber of molelcules
Total (without water)58,6701
Polymers58,6701
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)127.518, 127.518, 89.782
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Detailsbiological unit is the same as asym.

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Components

#1: Protein Importin subunit alpha /


Mass: 58669.914 Da / Num. of mol.: 1 / Fragment: armadillo repeat domian
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: MOS6, At4g02150 / Plasmid: pOPIN-F / Production host: Escherichia coli (E. coli) / Strain (production host): SoluBL21 / References: UniProt: Q4JHM3, UniProt: O04294*PLUS

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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: 2.39 Å3/Da / Density % sol: 48.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.2 M Mg-acetate, 0.1 M MES pH 6.5, 19% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.976 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.9→69.66 Å / Num. obs: 11858 / % possible obs: 98.3 % / Redundancy: 2.7 % / Net I/σ(I): 8.8
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 2.6 / % possible all: 98.8

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Processing

Software
NameVersionClassification
iMOSFLM1.0.7data reduction
REFMAC5.8.0071refinement
PDB_EXTRACT3.14data extraction
RefinementResolution: 2.9→69.66 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.935 / SU B: 54.117 / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.411 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2626 562 4.8 %RANDOM
Rwork0.2186 11264 --
obs0.2207 11826 97.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 165.92 Å2 / Biso mean: 106.386 Å2 / Biso min: 72.46 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20.39 Å20 Å2
2--0.78 Å20 Å2
3----2.52 Å2
Refinement stepCycle: final / Resolution: 2.9→69.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3138 0 0 0 3138
Num. residues----407
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.023188
X-RAY DIFFRACTIONr_bond_other_d0.0010.023113
X-RAY DIFFRACTIONr_angle_refined_deg0.781.9684336
X-RAY DIFFRACTIONr_angle_other_deg0.68237171
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6795402
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.39326.519135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.12815562
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6661510
X-RAY DIFFRACTIONr_chiral_restr0.0410.2520
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213590
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02658
X-RAY DIFFRACTIONr_mcbond_it1.2518.2321623
X-RAY DIFFRACTIONr_mcbond_other1.2518.2321622
X-RAY DIFFRACTIONr_mcangle_it2.1512.3472020
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 40 -
Rwork0.335 838 -
all-878 -
obs--98.54 %
Refinement TLS params.Method: refined / Origin x: 120.084 Å / Origin y: 40.6651 Å / Origin z: 21.2515 Å
111213212223313233
T0.1884 Å20.0297 Å2-0.0283 Å2-0.0734 Å2-0.0165 Å2--0.0785 Å2
L4.2716 °20.7273 °2-3.1153 °2-0.2329 °2-0.7561 °2--3.1559 °2
S0.2293 Å °0.0044 Å °0.41 Å °0.0459 Å °-0.0787 Å °0.0574 Å °-0.3752 Å °0.0732 Å °-0.1506 Å °

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