3FFE | pdb_00003ffe

Structure of Achromobactin Synthetase Protein D, (AcsD)

PDB DOI: https://doi.org/10.2210/pdb3FFE/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Dickeya chrysanthemi
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-12-03 Released: 2009-02-03
Deposition Author(s): McMahon, S.A., Liu, H., Carter, L., Oke, M., Johnson, K.A., Schmelz, S., Challis, G.L., White, M.F., Naismith, J.H., Scottish Structural Proteomics Facility (SSPF)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.241 (Depositor), 0.244 (DCC)
R-Value Work:
0.186 (Depositor), 0.190 (DCC)
R-Value Observed:
0.189 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

AcsD catalyzes enantioselective citrate desymmetrization in siderophore biosynthesis

Schmelz, S., Kadi, N., McMahon, S.A., Song, L., Oves-Costales, D., Oke, M., Liu, H., Johnson, K.A., Carter, L.G., Botting, C.H., White, M.F., Challis, G.L., Naismith, J.H.

(2009) Nat Chem Biol 5: 174-182

PubMed: 19219015 Search on PubMed
DOI: https://doi.org/10.1038/nchembio0309-143
Primary Citation Related Structures:
3FFE

Macromolecule Content

Total Structure Weight: 148.78 kDa
Atom Count: 9,754
Modeled Residue Count: 1,149
Deposited Residue Count: 1,306
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AcsD	A, B	653	Dickeya chrysanthemi	Mutation(s): 0 Gene Names: acsD
UniProt
Find proteins for Q93AT8 (Dickeya chrysanthemi) Explore Q93AT8 Go to UniProtKB: Q93AT8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q93AT8
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.241 (Depositor), 0.244 (DCC)
R-Value Work: 0.186 (Depositor), 0.190 (DCC)
R-Value Observed: 0.189 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.328	α = 90
b = 95.729	β = 90
c = 160.52	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
SHELXS	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-02-03

Deposition Author(s):

Scottish Structural Proteomics Facility (SSPF)

Revision History (Full details and data files)

Version 1.0: 2009-02-03
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2023-12-27
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.