7BQW | pdb_00007bqw

Crystal structure of Methionine gamma-lyase from Fusobacterium nucleatum

PDB DOI: https://doi.org/10.2210/pdb7BQW/pdb

Classification: LYASE
Organism(s): Fusobacterium nucleatum subsp. nucleatum ATCC 25586
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-03-25 Released: 2020-04-15
Deposition Author(s): Lan, J., Chen, Y., Liu, W., Xu, Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.278 (Depositor), 0.279 (DCC)
R-Value Work:
0.214 (Depositor), 0.215 (DCC)
R-Value Observed:
0.217 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of Methionine gamma-lyase from Fusobacterium nucleatum

Lan, J., Liu, W., Chen, Y., Xu, Y.

To be published.

Macromolecule Content

Total Structure Weight: 173.43 kDa
Atom Count: 10,958
Modeled Residue Count: 1,415
Deposited Residue Count: 1,580
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-methionine gamma-lyase	A, B, C, D	395	Fusobacterium nucleatum subsp. nucleatum ATCC 25586	Mutation(s): 0 Gene Names: FN1419 EC: 4.4.1.11 (PDB Primary Data), 4.4.1.2 (PDB Primary Data), 4.4.1.28 (PDB Primary Data)
UniProt
Find proteins for Q8RDT4 (Fusobacterium nucleatum subsp. nucleatum (strain ATCC 25586 / DSM 15643 / BCRC 10681 / CIP 101130 / JCM 8532 / KCTC 2640 / LMG 13131 / VPI 4355)) Explore Q8RDT4 Go to UniProtKB: Q8RDT4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8RDT4
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.278 (Depositor), 0.279 (DCC)
R-Value Work: 0.214 (Depositor), 0.215 (DCC)
R-Value Observed: 0.217 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.205	α = 90
b = 95.205	β = 90
c = 302.253	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-04-15

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31200556
National Natural Science Foundation of China (NSFC)	China	21272031

Revision History (Full details and data files)

Version 1.0: 2020-04-15
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Database references, 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.