5Z8T | pdb_00005z8t

Flavin-containing monooxygenase

PDB DOI: https://doi.org/10.2210/pdb5Z8T/pdb
Entry: 5Z8T supersedes: 5GJ8

Classification: OXIDOREDUCTASE
Organism(s): Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-02-01 Released: 2019-02-06
Deposition Author(s): Choe, J., Moon, H., Shin, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.33 Å
R-Value Free:
0.256 (Depositor), 0.262 (DCC)
R-Value Work:
0.222 (Depositor), 0.229 (DCC)
R-Value Observed:
0.224 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5Z8T

Ligand Structure Quality Assessment

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

Literature

Crystal structure of putative Flavin-dependent monooxgenase

Choe, J., Moon, H., Shin, S.

To be published.

Macromolecule Content

Total Structure Weight: 134.18 kDa
Atom Count: 9,957
Modeled Residue Count: 1,185
Deposited Residue Count: 1,197
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acyl-CoA dehydrogenase type 2 domain protein	A, B, C	399	Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446	Mutation(s): 0 Gene Names: Aaci_0955
UniProt
Find proteins for C8WV06 (Alicyclobacillus acidocaldarius subsp. acidocaldarius (strain ATCC 27009 / DSM 446 / BCRC 14685 / JCM 5260 / KCTC 1825 / NBRC 15652 / NCIMB 11725 / NRRL B-14509 / 104-IA)) Explore C8WV06 Go to UniProtKB: C8WV06
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C8WV06
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD (Subject of Investigation/LOI) Query on FAD Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth B] SDF format, chain F [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth C] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B] mmCIF format, chain F [auth C]	D [auth A], E [auth B], F [auth C]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.33 Å
R-Value Free: 0.256 (Depositor), 0.262 (DCC)
R-Value Work: 0.222 (Depositor), 0.229 (DCC)
R-Value Observed: 0.224 (Depositor)

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 177.256	α = 90
b = 177.256	β = 90
c = 285.322	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
MOLREP	phasing
HKL-2000	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2019-02-06

Deposition Author(s):

This entry supersedes: 5GJ8

Revision History (Full details and data files)

Version 1.0: 2019-02-06
Type: Initial release
Version 1.1: 2023-11-22
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.