5NHI | pdb_00005nhi

Crystal structure of the Escherichia coli N-terminal domain of DsbD (nDsbD) without the cap-loop region

PDB DOI: https://doi.org/10.2210/pdb5NHI/pdb

Classification: OXIDOREDUCTASE
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2017-03-21 Released: 2018-02-28
Deposition Author(s): Saridakis, E., Stelzl, L.S., Mavridou, D.A.I., Redfield, C.
Funding Organization(s): Wellcome Trust, Medical Research Council (United Kingdom)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.292 (Depositor), 0.282 (DCC)
R-Value Work:
0.252 (Depositor), 0.256 (DCC)
R-Value Observed:
0.254 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of the Escherichia coli N-terminal domain of DsbD (nDsbD) without the cap-loop region

Stelzl, L.S., Mavridou, D.A.I., Saridakis, E., Redfield, C.

To be published.

Macromolecule Content

Total Structure Weight: 29.59 kDa
Atom Count: 1,838
Modeled Residue Count: 224
Deposited Residue Count: 268
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thiol:disulfide interchange protein DsbD	A, B	134	Escherichia coli	Mutation(s): 2 Gene Names: dsbD, EL75_4028, EL79_4206, EL80_4122 EC: 1.8.1.8
UniProt
Find proteins for P36655 (Escherichia coli (strain K12)) Explore P36655 Go to UniProtKB: P36655
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P36655
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.292 (Depositor), 0.282 (DCC)
R-Value Work: 0.252 (Depositor), 0.256 (DCC)
R-Value Observed: 0.254 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.332	α = 90
b = 81.338	β = 100.66
c = 46.394	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-02-28

Deposition Author(s):

Mavridou, D.A.I.

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	092532
Medical Research Council (United Kingdom)	United Kingdom	MR/M009505/1

Revision History (Full details and data files)

Version 1.0: 2018-02-28
Type: Initial release
Version 1.1: 2019-10-16
Changes: Data collection
Version 1.2: 2024-01-17
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-11-20
Changes: 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.