6KGZ

bacterial cystathionine gamma-lyase MccB of Staphylococcus aureus

PDB DOI: https://doi.org/10.2210/pdb6KGZ/pdb

Classification: LYASE
Organism(s): Staphylococcus aureus subsp. aureus Mu50
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-07-12 Released: 2020-03-25
Deposition Author(s): Ha, N.-C., Lee, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.236
R-Value Work: 0.210
R-Value Observed: 0.212

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of Bacterial Cystathionine Gamma-Lyase in The Cysteine Biosynthesis Pathway of Staphylococcus aureus

Lee, D., Jeong, S., Ahn, J., Ha, N.-C., Kwon, A.-R.

(2019) Crystals (Basel) 9: 656-656

DOI: https://doi.org/10.3390/cryst9120656

Macromolecule Content

Total Structure Weight: 43.46 kDa
Atom Count: 2,861
Modelled Residue Count: 368
Deposited Residue Count: 397
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cystathionine gamma-lyase	A	397	Staphylococcus aureus subsp. aureus Mu50	Mutation(s): 0 Gene Names: yrhB, SAV0460 EC: 4.4.1.1
UniProt
Find proteins for A0A0H3JQ19 (Staphylococcus aureus (strain Mu50 / ATCC 700699)) Explore A0A0H3JQ19 Go to UniProtKB: A0A0H3JQ19
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H3JQ19
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS Query on TRS 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]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.236
R-Value Work: 0.210
R-Value Observed: 0.212
Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.567	α = 90
b = 105.567	β = 90
c = 287.986	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2020-03-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-03-25
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, 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.