5NBG | pdb_00005nbg

Structure of the cytoplasmic domain I of OutF in the D. dadantii type II secretion system

PDB DOI: https://doi.org/10.2210/pdb5NBG/pdb

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

Deposited: 2017-03-01 Released: 2018-03-21
Deposition Author(s): Zhang, H., Gu, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.265 (Depositor), 0.261 (DCC)
R-Value Work:
0.210 (Depositor)
R-Value Observed:
0.215 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Structure of the first cytoplasmic domain of OutF and assembly of the inner-membrane platform proteins of the D. dadantii type II secretion system

Zhang, H., Gu, S.

To be published.

Macromolecule Content

Total Structure Weight: 23.33 kDa
Atom Count: 1,652
Modeled Residue Count: 214
Deposited Residue Count: 218
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
General secretion pathway protein F	A, B	109	Dickeya dadantii 3937	Mutation(s): 0 Gene Names: outF, Dda3937_02417
UniProt
Find proteins for E0SM39 (Dickeya dadantii (strain 3937)) Explore E0SM39 Go to UniProtKB: E0SM39
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	E0SM39
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.265 (Depositor), 0.261 (DCC)
R-Value Work: 0.210 (Depositor)
R-Value Observed: 0.215 (Depositor)

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.175	α = 90
b = 116.175	β = 90
c = 47.998	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
MOLREP	phasing
Aimless	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2018-03-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-03-21
Type: Initial release
Version 1.1: 2024-01-17
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.