3A2E

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), 0.230 (DCC)
R-Value Work:
0.207 (Depositor), 0.210 (DCC)
R-Value Observed:
0.208 (Depositor)

wwPDB Validation 3D Report Full Report

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 of 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
Modelled Residue Count: 432
Deposited Residue Count: 432
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A4ZDL6
Sequence Annotations Expand
Reference Sequence LOADING

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.38 Å
R-Value Free: 0.232 (Depositor), 0.230 (DCC)
R-Value Work: 0.207 (Depositor), 0.210 (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

View Full Validation Report

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