7EG5 | pdb_00007eg5

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 (Depositor), 0.240 (DCC)
R-Value Work:
0.199 (Depositor), 0.210 (DCC)
R-Value Observed:
0.200 (Depositor)

Starting Model: experimental
View more details

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
Modeled 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 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: 1.96 Å
R-Value Free: 0.228 (Depositor), 0.240 (DCC)
R-Value Work: 0.199 (Depositor), 0.210 (DCC)
R-Value Observed: 0.200 (Depositor)

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

View Full Validation Report

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 R01GM157729.