7EG5

FMN-bound form of YviC from Lactococcus lactis subsp. lactis Il1403

PDB DOI: https://doi.org/10.2210/pdb7EG5/pdb

Classification: FLAVOPROTEIN
Organism(s): Lactococcus lactis subsp. lactis Il1403
Expression System: Escherichia coli K-12
Mutation(s): No

Deposited: 2021-03-24 Released: 2022-04-20
Deposition Author(s): Sugiura, N., Nakanishi, T., Kitamura, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.96 Å
R-Value Free: 0.228
R-Value Work: 0.199
R-Value Observed: 0.200

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

FMN-bound form of YviC from Lactococcus lactis subsp. lactis Il1403

Sugiura, N., Nakanishi, T., Kitamura, M.

To be published.

Macromolecule Content

Total Structure Weight: 29.21 kDa
Atom Count: 2,064
Modelled Residue Count: 250
Deposited Residue Count: 250
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FMN-binding protein	A, B	125	Lactococcus lactis subsp. lactis Il1403	Mutation(s): 0 Gene Names: yviC, L164222
UniProt
Find proteins for Q9CDV0 (Lactococcus lactis subsp. lactis (strain IL1403)) Explore Q9CDV0 Go to UniProtKB: Q9CDV0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9CDV0
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 C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	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: 1.96 Å
R-Value Free: 0.228
R-Value Work: 0.199
R-Value Observed: 0.200
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.509	α = 90
b = 94.801	β = 90
c = 142.075	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2022-04-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2022-04-20
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, 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 R01GM133198.