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.

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Experimental Data Snapshot

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

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

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

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

Experimental Data & Validation

Experimental Data

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

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2017-03-29
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description