6ASL | pdb_00006asl

Crystal Structure of Flavin monooxygenase CmoJ (earlier YtnJ) bound with FMN

PDB DOI: https://doi.org/10.2210/pdb6ASL/pdb

Classification: FLAVOPROTEIN
Organism(s): Bacillus subtilis subsp. subtilis str. 168
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-08-24 Released: 2018-09-12
Deposition Author(s): Bhandari, D.M., Zhao, B., Li, P., Begley, T.P.
Funding Organization(s): Robert A. Welch Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.201 (Depositor), 0.200 (DCC)
R-Value Work:
0.172 (Depositor), 0.170 (DCC)
R-Value Observed:
0.173 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Flavin mediated Pummerer type rearrangement in cysteine salvage pathway

Bhandari, D.M., Krishnamoorthy, K., Zhao, B., Li, P., Begley, T.P.

To be published.

Macromolecule Content

Total Structure Weight: 50.38 kDa
Atom Count: 3,673
Modeled Residue Count: 430
Deposited Residue Count: 444
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative monooxygenase MoxC	A	444	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0 Gene Names: moxC, ytnJ, BSU29310 EC: 1.14.14
UniProt
Find proteins for O34974 (Bacillus subtilis (strain 168)) Explore O34974 Go to UniProtKB: O34974
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O34974
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN Query on FMN 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 MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
LFN Query on LFN 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]	LUMIFLAVIN C₁₃ H₁₂ N₄ O₂ KPDQZGKJTJRBGU-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.201 (Depositor), 0.200 (DCC)
R-Value Work: 0.172 (Depositor), 0.170 (DCC)
R-Value Observed: 0.173 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.079	α = 90
b = 87.079	β = 90
c = 194.94	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	phasing
Coot	model building
iMOSFLM	data reduction
PHENIX	model building

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2018-09-12

Deposition Author(s):

Funding Organization	Location	Grant Number
Robert A. Welch Foundation	United States	A-0034

Revision History (Full details and data files)

Version 1.0: 2018-09-12
Type: Initial release
Version 1.1: 2023-10-04
Changes: Data collection, Database references, Refinement description

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.