2REM | pdb_00002rem

Crystal Structure of oxidoreductase DsbA from Xylella fastidiosa

PDB DOI: https://doi.org/10.2210/pdb2REM/pdb

Classification: OXIDOREDUCTASE
Organism(s): Xylella fastidiosa
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-09-26 Released: 2008-10-07
Deposition Author(s): Rinaldi, F.C., Guimaraes, B.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.224 (Depositor), 0.222 (DCC)
R-Value Work:
0.183 (Depositor), 0.183 (DCC)
R-Value Observed:
0.185 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Residues substitution in the active site of DSBA may compensate for the lack of the canonical motif CPHC

Rinaldi, F.C., Guimaraes, B.G.

To be published.

Macromolecule Content

Total Structure Weight: 64.7 kDa
Atom Count: 4,974
Modeled Residue Count: 576
Deposited Residue Count: 587
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Disulfide oxidoreductase	A, B, C	193	Xylella fastidiosa	Mutation(s): 0 Gene Names: XF1436 EC: 1.8.4.2
UniProt
Find proteins for Q9PDE3 (Xylella fastidiosa (strain 9a5c)) Explore Q9PDE3 Go to UniProtKB: Q9PDE3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9PDE3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
8 residue peptide	D [auth T]	8	Xylella fastidiosa	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
UNK Query on UNK	D [auth T]	L-PEPTIDE LINKING	C₄ H₉ N O₂		--

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.224 (Depositor), 0.222 (DCC)
R-Value Work: 0.183 (Depositor), 0.183 (DCC)
R-Value Observed: 0.185 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 200.117	α = 90
b = 41.722	β = 95.87
c = 79.807	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-10-07

Deposition Author(s):

Guimaraes, B.G.

Revision History (Full details and data files)

Version 1.0: 2008-10-07
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Advisory, Refinement description
Version 1.3: 2024-02-21
Changes: Advisory, Data collection, Database references