3A5F | pdb_00003a5f

High-resolution structure of DHDPS from Clostridium botulinum in complex with pyruvate

PDB DOI: https://doi.org/10.2210/pdb3A5F/pdb

Classification: LYASE
Organism(s): Clostridium botulinum A str. ATCC 19397
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2009-08-06 Released: 2010-06-30
Deposition Author(s): Atkinson, S.C., Dobson, R.C.J., Perugini, M.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.19 Å
R-Value Free:
0.140 (Depositor), 0.150 (DCC)
R-Value Work:
0.112 (Depositor)
R-Value Observed:
0.113 (Depositor)

Starting Model: experimental
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This is version 1.4 of the entry. See complete history.

Literature

The high resolution structure of DHDPS from Clostridium botulinum

Dobson, R.C.J., Atkinson, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 63.43 kDa
Atom Count: 5,606
Modeled Residue Count: 582
Deposited Residue Count: 582
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrodipicolinate synthase	A, B	291	Clostridium botulinum A str. ATCC 19397	Mutation(s): 0 Gene Names: dapA EC: 4.2.1.52

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KPI Query on KPI	A, B	L-PEPTIDE LINKING	C₉ H₁₆ N₂ O₄		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.19 Å
R-Value Free: 0.140 (Depositor), 0.150 (DCC)
R-Value Work: 0.112 (Depositor)
R-Value Observed: 0.113 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.358	α = 90
b = 54.836	β = 126.29
c = 94.304	γ = 90

Software Package:

Software Name	Purpose
PHASES	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-06-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-06-30
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2012-12-26
Changes: Structure summary
Version 1.3: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2023-11-29
Changes: Data collection

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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.