4BQK | pdb_00004bqk

rice importin_alpha : VirD2NLS complex

PDB DOI: https://doi.org/10.2210/pdb4BQK/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Oryza sativa, Agrobacterium tumefaciens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-05-31 Released: 2014-02-19
Deposition Author(s): Chang, C.-W., Counago, R.M., Williams, S.J., Kobe, B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.224 (Depositor), 0.222 (DCC)
R-Value Work:
0.196 (Depositor), 0.218 (DCC)
R-Value Observed:
0.197 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

Structural Basis of Interaction of Bipartite Nuclear Localization Signal from Agrobacterium Vird2 with Rice Importin-Alpha

Chang, C.-W., Williams, S.J., Counago, R.M., Kobe, B.

(2014) Mol Plant 7: 1061

PubMed: 24503158 Search on PubMed
DOI: https://doi.org/10.1093/mp/ssu014
Primary Citation Related Structures:
4BPL, 4BQK

Organizational Affiliation

School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience, and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Qld 4072, Australia.

Macromolecule Content

Total Structure Weight: 104.65 kDa
Atom Count: 7,163
Modeled Residue Count: 872
Deposited Residue Count: 952
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IMPORTIN SUBUNIT ALPHA-1A	A, B	456	Oryza sativa	Mutation(s): 0
UniProt
Find proteins for Q71VM4 (Oryza sativa subsp. japonica) Explore Q71VM4 Go to UniProtKB: Q71VM4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q71VM4
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
T-DNA BORDER ENDONUCLEASE VIRD2	C, D	20	Agrobacterium tumefaciens	Mutation(s): 0 EC: 3.1
UniProt
Find proteins for P18592 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore P18592 Go to UniProtKB: P18592
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P18592
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth B] E [auth A], F [auth A], G [auth A], H [auth A], I [auth B], J [auth B], K [auth B], L [auth B], M [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.224 (Depositor), 0.222 (DCC)
R-Value Work: 0.196 (Depositor), 0.218 (DCC)
R-Value Observed: 0.197 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.803	α = 90
b = 140.948	β = 90
c = 72.632	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-02-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-02-19
Type: Initial release
Version 1.1: 2014-06-18
Changes: Database references
Version 2.0: 2023-12-20
Changes: Atomic model, Data collection, Database references, Derived calculations, Other, Refinement description