5IL5 | pdb_00005il5

Crystal structure of the dehydratase domain of MlnD from Bacillus amyloliquefaciens

PDB DOI: https://doi.org/10.2210/pdb5IL5/pdb

Classification: LYASE
Organism(s): Bacillus velezensis FZB42
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-03-04 Released: 2017-03-29
Deposition Author(s): Jakob, R.P., Herbst, D.A., Maier, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.91 Å
R-Value Free:
0.270 (Depositor), 0.255 (DCC)
R-Value Work:
0.228 (Depositor)
R-Value Observed:
0.230 (Depositor)

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

Literature

Crystal Structures of Dehydratase Domains from trans-AT Polyketide Biosynthetic Pathways

Jakob, R.P., Muller, R., Herbst, D.A., Maier, T.

To be published.

Macromolecule Content

Total Structure Weight: 69.89 kDa
Atom Count: 4,140
Modeled Residue Count: 510
Deposited Residue Count: 624
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MlnD	A, B	312	Bacillus velezensis FZB42	Mutation(s): 0 Gene Names: mlnD, RBAM_014360
UniProt
Find proteins for A7Z473 (Bacillus velezensis (strain DSM 23117 / BGSC 10A6 / LMG 26770 / FZB42)) Explore A7Z473 Go to UniProtKB: A7Z473
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A7Z473
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.91 Å
R-Value Free: 0.270 (Depositor), 0.255 (DCC)
R-Value Work: 0.228 (Depositor)
R-Value Observed: 0.230 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.05	α = 90
b = 37.95	β = 92.28
c = 166.46	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2017-03-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-03-29
Type: Initial release
Version 1.1: 2024-01-10
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.