8Z12 | pdb_00008z12

Crystal structure of WT DiatB

PDB DOI: https://doi.org/10.2210/pdb8Z12/pdb

Classification: OXIDOREDUCTASE
Organism(s): Streptomyces ardesiacus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-04-10 Released: 2025-02-19
Deposition Author(s): Peng, M., Wu, Q.L.
Funding Organization(s): National Science Foundation (NSF, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.24 Å
R-Value Free:
0.249 (Depositor), 0.240 (DCC)
R-Value Work:
0.205 (Depositor), 0.211 (DCC)
R-Value Observed:
0.208 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Bacterial Biosynthesis of Nitrile-Containing Natural Products: Basis for Recognition of Diversified Substrates

Peng, M., Wu, Q., Ma, L., Teng, Z.J., Hou, X., Zhu, H., Ju, J.

(2024) ACS Catal 14: 17780-17793

DOI: https://doi.org/10.1021/acscatal.4c06581

Macromolecule Content

Total Structure Weight: 47.83 kDa
Atom Count: 3,471
Modeled Residue Count: 426
Deposited Residue Count: 432
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Flavin-dependent monooxygenase	A	432	Streptomyces ardesiacus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
FLC Query on FLC Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.24 Å
R-Value Free: 0.249 (Depositor), 0.240 (DCC)
R-Value Work: 0.205 (Depositor), 0.211 (DCC)
R-Value Observed: 0.208 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.846	α = 90
b = 66.846	β = 90
c = 376.751	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-02-19

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	--

Revision History (Full details and data files)

Version 1.0: 2025-02-19
Type: Initial release

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.