4WFW | pdb_00004wfw

The crystal structure of Dickeya dadantii GspB from the type 2 secretion system

PDB DOI: https://doi.org/10.2210/pdb4WFW/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Dickeya dadantii 3937
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-09-17 Released: 2015-09-30
Deposition Author(s): Rycroft, P.B., Pickersgill, R.W., Shevchik, V.E.
Funding Organization(s): Biotechnology and Biological Sciences Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.254 (Depositor), 0.253 (DCC)
R-Value Work:
0.209 (Depositor), 0.220 (DCC)
R-Value Observed:
0.213 (Depositor)

Starting Model: experimental
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This is version 2.1 of the entry. See complete history.

Literature

The crystal structure of Dickeya dadantii GspB from the type 2 secretion system

Rycroft, P.B.

To be published.

Macromolecule Content

Total Structure Weight: 9.92 kDa
Atom Count: 676
Modeled Residue Count: 84
Deposited Residue Count: 90
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
General secretion pathway protein B	A	90	Dickeya dadantii 3937	Mutation(s): 0 Gene Names: outB, Dda3937_02412
UniProt
Find proteins for Q01563 (Dickeya dadantii (strain 3937)) Explore Q01563 Go to UniProtKB: Q01563
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q01563
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.254 (Depositor), 0.253 (DCC)
R-Value Work: 0.209 (Depositor), 0.220 (DCC)
R-Value Observed: 0.213 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.21	α = 90
b = 36.21	β = 90
c = 131.28	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2015-09-30

Deposition Author(s):

Pickersgill, R.W.

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/I013334/1

Revision History (Full details and data files)

Version 1.0: 2015-09-30
Type: Initial release
Version 2.0: 2017-08-30
Changes: Advisory, Atomic model, Author supporting evidence
Version 2.1: 2024-01-10
Changes: Data collection, Database references, Refinement description

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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.