SAXSdb — 6kgz

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Cystathionine gamma-lyase

Staphylococcus aureus subsp. aureus Mu50

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–380	Not recorded	TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；311 K；Tacsimate, PEG 3350	Resolution 2.30 Å R-free 0.236

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 6KGZ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6KHQ bacterial cystathionine gamma-lyase MccB of Staphylococcus aureus with cofactor PLP Deposited 2019-07-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–380（380 aa） Chain B 1–380（380 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；288 K；PEG 400, Sodium Acetate	Resolution 2.30 Å R-free 0.249
9J7P Crystal structure of S. aureus MccB mutant S323A Deposited 2024-08-19	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–380（380 aa）	Mutation：S323A	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；287.15 K；0.1 M HEPES pH 7.5, 2% PEG400, 2 M ammonium sulfate	Resolution 2.19 Å R-free 0.223
9J7Q Crystal structure of S. aureus MccB with PLP Deposited 2024-08-19	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–380（380 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	PEG DI(HYDROXYETHYL)ETHER × 16	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；287.15 K；0.1M Sodium Acetate trihydrate pH4.5, 30% PEG 300	Resolution 1.64 Å R-free 0.201
9J7R Crystal structure of S. aureus MccB mutant K196A Deposited 2024-08-19	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–380（380 aa） Chain B 1–380（380 aa）	Mutation：K196A Mutation：K196A	PGU N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-glutamic acid × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；287.15 K；0.1 M sodium citrate pH 5.5, 22% PEG1000	Resolution 2.50 Å R-free 0.266
9XLU Crystal structure of Staphylococcus aureus cystathionine gamma-lyase V129G Deposited 2025-11-08	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–380（380 aa）	Mutation：V129G	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；287.15 K；16% PEG 3350, 1.5% tryptone, 0.05M HEPES sodium pH 7.0, 0.01M sodium azide	Resolution 2.33 Å R-free 0.260

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A0H3JQ19_STAAM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 18–397； UniProt 1–380

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6kgz
Deposition date deposition_date	2019-07-12
Structure title title	bacterial cystathionine gamma-lyase MccB of Staphylococcus aureus
Keywords keywords	Cysteine biosynthesis pathway, MccB, PLP binding protein, Schiff-base, yhrB, LYASE; LYASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	22.10 Å
Radius of gyration Rg (electron density) rg_electron	21.03 Å
Forward intensity I(0) i0	26708700.00
Molecular weight molecular_weight	39913.0 kDa
Excluded volume excluded_volume	50202 Å³
Envelope volume envelope_volume	59399 Å³
Hydration-shell volume shell_volume	23456 Å³
Envelope diameter envelope_diameter	83.2 Å
Shell Rg shell_rg	27.90 Å
Envelope Rg envelope_rg	21.63 Å
Shape Rg shape_rg	21.04 Å
Total Rg total_rg	21.90 Å
Total atoms total_atoms	2809
Residues n_residues	368
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	77.2 Å
Rg (real space) rg_real	22.04 Å
Rg uncertainty (real space) rg_real_error	0.60 Å
I(0) (real space) i0_real	2.6710e+07
I(0) uncertainty (real space) i0_real_error	3.5210e+05
Rg (reciprocal space) rg_reciprocal	22.05 Å
I(0) (reciprocal space) i0_reciprocal	26710000.0000
Solution quality estimate total_estimate	0.6083
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	26.5 Å
Skewness Skewness skewness	0.326
Kurtosis Kurtosis kurtosis	-0.161
Angular range angular_range	— – 0.3600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6307000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.717; Stabil: 0.999; Sysdev: 0.262; Positv: 1.000; Valcen: 0.968; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Cystathionine gamma-lyase
Molecular weight formula_weight	43336.9 kDa
EC 编号 ec_number	4.4.1.1
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2861

MHHHHHHENLYFQGAASMNKKTKLIHGGHTTDDYTGAVTTPIYQTSTYLQDDIGDLRQGYEYSRTANPTRSSVESVIAALENGKHGFAFSSGVAAISAVVMLLDKGDHIILNSDVYGGTYRALTKVFTRFGIEVDFVDTTHTDSIVQAIRPTTKMLFIETPSNPLLRVTDIKKSAEIAKEHGLISVVDNTFMTPYYQNPLDLGIDIVLHSATKYLGGHSDVVAGLVATSDDKLAERLAFISNSTGGILGPQDSYLLVRGIKTLGLRMEQINRSVIEIIKMLQAHPAVQQVFHPSIESHLNHDVHMAQADGHTGVIAFEVKNTESAKQLIKATSYYTLAESLGAVESLISVPALMTHASIPADIRAKEGITDGLVRISVGIEDTEDLVDDLKQALDTL

来源 Source

来源生物 organism	Staphylococcus aureus subsp. aureus Mu50
NCBI Class编号 ncbi_taxonomy_id	158878
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	52

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d6kgza_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamily	c.67.1 — PLP-dependent transferases
Family Family family	c.67.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	6kgzA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

Domain ID domain_id	6kgzA02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

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8. Citations (1)

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Unit-cell length a length_a	105.567 Å
Unit-cell length b length_b	105.567 Å
Unit-cell length c length_c	287.986 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	I 41 2 2
Space-group number int_tables_number	98
Crystal system crystal_system	tetragonal

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	46.590 Å
R factor r_factor	0.2116
R_work r_work	0.2102
R_free r_free	0.2364

fit	/app/data/saxs_computation/kg/6kgz/6kgz.fit
pddf	/app/data/pr_computation/kg/6kgz/6kgz.pr.out
profile	/app/data/saxs_computation/kg/6kgz/6kgz.dat

bacterial cystathionine gamma-lyase MccB of Staphylococcus aureus

1. Protein Identity and Related Structures Protein Identity & Related Structures

Cystathionine gamma-lyase

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction