3PSM | pdb_00003psm

.98A crystal structure of a dimeric plant defensin SPE10

PDB DOI: https://doi.org/10.2210/pdb3PSM/pdb

Classification: ANTIMICROBIAL PROTEIN
Organism(s): Pachyrhizus erosus
Mutation(s): No

Deposited: 2010-12-01 Released: 2010-12-29
Deposition Author(s): Zhou, H., Song, X., Gong, W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 0.98 Å
R-Value Free:
0.164 (Depositor)
R-Value Work:
0.120 (Depositor), 0.150 (DCC)
R-Value Observed:
0.125 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

0.98A crystal structure of a dimeric plant defensin SPE10

Zhou, H., Song, X., Gong, W.

To be published.

Macromolecule Content

Total Structure Weight: 11.02 kDa
Atom Count: 955
Modeled Residue Count: 94
Deposited Residue Count: 94
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Defensin	A, B	47	Pachyrhizus erosus	Mutation(s): 0
UniProt
Find proteins for Q6B519 (Pachyrhizus erosus) Explore Q6B519 Go to UniProtKB: Q6B519
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6B519
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 0.98 Å
R-Value Free: 0.164 (Depositor)
R-Value Work: 0.120 (Depositor), 0.150 (DCC)
R-Value Observed: 0.125 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.714	α = 90
b = 28.111	β = 103.78
c = 54.853	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
Shake	model building
SHELXL-97	refinement
HKL-2000	data reduction
HKL-2000	data scaling
Shake	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-12-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-12-29
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-10-09
Changes: Data collection, Database references, Structure summary

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.