3A2E | pdb_00003a2e

Crystal structure of ginkbilobin-2, the novel antifungal protein from Ginkgo biloba seeds

PDB DOI: https://doi.org/10.2210/pdb3A2E/pdb
Entry: 3A2E supersedes: 2E79

Classification: PLANT PROTEIN
Organism(s): Ginkgo biloba
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2009-05-13 Released: 2009-06-02
Deposition Author(s): Miyakawa, T., Miyazono, K., Sawano, Y., Hatano, K., Tanokura, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.38 Å
R-Value Free:
0.232 (Depositor), 0.238 (DCC)
R-Value Work:
0.207 (Depositor), 0.212 (DCC)
R-Value Observed:
0.208 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3A2E

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of ginkbilobin-2 with homology to the extracellular domain of plant cysteine-rich receptor-like kinases

Miyakawa, T., Miyazono, K., Sawano, Y., Hatano, K., Tanokura, M.

(2009) Proteins 77: 247-251

PubMed: 19603485 Search on PubMed
DOI: https://doi.org/10.1002/prot.22494
Primary Citation Related Structures:
3A2E

Organizational Affiliation

Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.

Macromolecule Content

Total Structure Weight: 46.68 kDa
Atom Count: 3,742
Modeled Residue Count: 432
Deposited Residue Count: 432
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ginkbilobin-2	A, B, C, D	108	Ginkgo biloba	Mutation(s): 0
UniProt
Find proteins for A4ZDL6 (Ginkgo biloba) Explore A4ZDL6 Go to UniProtKB: A4ZDL6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A4ZDL6
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.38 Å
R-Value Free: 0.232 (Depositor), 0.238 (DCC)
R-Value Work: 0.207 (Depositor), 0.212 (DCC)
R-Value Observed: 0.208 (Depositor)

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.169	α = 90
b = 143.169	β = 90
c = 143.169	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXS	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-06-02

Deposition Author(s):

This entry supersedes: 2E79

Revision History (Full details and data files)

Version 1.0: 2009-06-02
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-10-30
Changes: Data collection, Database references, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.