6KGZ | pdb_00006kgz

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 (Depositor), 0.237 (DCC)
R-Value Work:
0.210 (Depositor), 0.211 (DCC)
R-Value Observed:
0.212 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6KGZ

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
Modeled Residue Count: 368
Deposited Residue Count: 397
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 (Depositor), 0.237 (DCC)
R-Value Work: 0.210 (Depositor), 0.211 (DCC)
R-Value Observed: 0.212 (Depositor)

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

View more in-depth experimental data

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 is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.