4Z38 | pdb_00004z38

Crystal structure of enoyl reductase domain of MlnA from the macrolactin biosynthesis cluster from Bacillus amyloliquefaciens

PDB DOI: https://doi.org/10.2210/pdb4Z38/pdb

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

Deposited: 2015-03-31 Released: 2016-04-13
Deposition Author(s): Jakob, R.P., Martin, S.F., Herbst, D.A., Maier, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.263 (Depositor), 0.274 (DCC)
R-Value Work:
0.246 (Depositor), 0.260 (DCC)
R-Value Observed:
0.247 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

The structural organization of trans-AT polyketide synthases: ketoacyl synthase and trans-acting enoyl reductase

Martin, S.F., Jakob, R.P., Herbst, D.A., Maier, T.

To be published.

Macromolecule Content

Total Structure Weight: 107.06 kDa
Atom Count: 7,159
Modeled Residue Count: 876
Deposited Residue Count: 940
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MlnA	A, B	470	Bacillus velezensis FZB42	Mutation(s): 0 Gene Names: mlnA, RBAM_014330 EC: 2.3.1.39
UniProt
Find proteins for A7Z470 (Bacillus velezensis (strain DSM 23117 / BGSC 10A6 / LMG 26770 / FZB42)) Explore A7Z470 Go to UniProtKB: A7Z470
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A7Z470
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN Query on FMN Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.263 (Depositor), 0.274 (DCC)
R-Value Work: 0.246 (Depositor), 0.260 (DCC)
R-Value Observed: 0.247 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.17	α = 90
b = 104.67	β = 90
c = 216.1	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-04-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-04-13
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.