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), 0.239 (DCC)
R-Value Work:
0.199 (Depositor), 0.207 (DCC)
R-Value Observed:
0.200 (Depositor)

Starting Model: experimental
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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

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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), 0.239 (DCC)
R-Value Work: 0.199 (Depositor), 0.207 (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

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Ligand Structure Quality Assessment

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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

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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.