5XHU | pdb_00005xhu

Crystal structure of ycgT from bacillus subtilis

PDB DOI: https://doi.org/10.2210/pdb5XHU/pdb

Classification: OXIDOREDUCTASE
Organism(s): Bacillus subtilis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-04-24 Released: 2018-05-02
Deposition Author(s): Komori, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.234 (Depositor), 0.236 (DCC)
R-Value Work:
0.201 (Depositor), 0.208 (DCC)
R-Value Observed:
0.203 (Depositor)

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Ligand Structure Quality Assessment

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

Literature

Crystal structure of ycgT from bacillus subtilis

Komori, H.

To be published.

Macromolecule Content

Total Structure Weight: 36.96 kDa
Atom Count: 2,686
Modeled Residue Count: 329
Deposited Residue Count: 329
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferredoxin--NADP reductase	A	329	Bacillus subtilis	Mutation(s): 0 Gene Names: B4417_2052 EC: 1.18.1.2
UniProt
Find proteins for O31475 (Bacillus subtilis (strain 168)) Explore O31475 Go to UniProtKB: O31475
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O31475
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD 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-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.234 (Depositor), 0.236 (DCC)
R-Value Work: 0.201 (Depositor), 0.208 (DCC)
R-Value Observed: 0.203 (Depositor)

Space Group: C 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.371	α = 90
b = 164.598	β = 90
c = 76.576	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
HKL	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2018-05-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-05-02
Type: Initial release
Version 1.1: 2024-03-27
Changes: Data collection, Database references

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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.