SAXSdb — 9xlu

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

Cystathionine gamma-synthase homolog

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	Mutation：V129G	No other associated polymer	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

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 9XLU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6KGZ bacterial cystathionine gamma-lyase MccB of Staphylococcus aureus Deposited 2019-07-12	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）	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
6KHQ bacterial cystathionine gamma-lyase MccB of Staphylococcus aureus with cofactor PLP Deposited 2019-07-16	Different construct Different mutation/modification 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

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	9xlu
Deposition date deposition_date	2025-11-08
Structure title title	Crystal structure of Staphylococcus aureus cystathionine gamma-lyase V129G
Keywords keywords	cystathionine gamma-lyase, PLP-dependent enzyme, transsulfuration, Staphylococcus aureus, 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	20.72 Å
Radius of gyration Rg (electron density) rg_electron	19.63 Å
Forward intensity I(0) i0	21945900.00
Molecular weight molecular_weight	36324.0 kDa
Excluded volume excluded_volume	45794 Å³
Envelope volume envelope_volume	52501 Å³
Hydration-shell volume shell_volume	21965 Å³
Envelope diameter envelope_diameter	65.5 Å
Shell Rg shell_rg	26.45 Å
Envelope Rg envelope_rg	19.81 Å
Shape Rg shape_rg	19.62 Å
Total Rg total_rg	20.57 Å
Total atoms total_atoms	2556
Residues n_residues	337
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	64.8 Å
Rg (real space) rg_real	20.61 Å
Rg uncertainty (real space) rg_real_error	0.35 Å
I(0) (real space) i0_real	2.1950e+07
I(0) uncertainty (real space) i0_real_error	2.9200e+05
Rg (reciprocal space) rg_reciprocal	20.63 Å
I(0) (reciprocal space) i0_reciprocal	21950000.0000
Solution quality estimate total_estimate	0.9005
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.3 Å
Skewness Skewness skewness	0.174
Kurtosis Kurtosis kurtosis	-0.430
Angular range angular_range	— – 0.3850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4852000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.905; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.995

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Cystathionine gamma-synthase homolog
Molecular weight formula_weight	43294.8 kDa
Mutation mutation	V129G
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	2782

MHHHHHHENLYFQGAASMNKKTKLIHGGHTTDDYTGAVTTPIYQTSTYLQDDIGDLRQGYEYSRTANPTRSSVESVIAALENGKHGFAFSSGVAAISAVVMLLDKGDHIILNSDVYGGTYRALTKVFTRFGIEVDFVDTTHTDSIGQAIRPTTKMLFIETPSNPLLRVTDIKKSAEIAKEHGLISVVDNTFMTPYYQNPLDLGIDIVLHSATKYLGGHSDVVAGLVATSDDKLAERLAFISNSTGGILGPQDSYLLVRGIKTLGLRMEQINRSVIEIIKMLQAHPAVQQVFHPSIESHLNHDVHMAQADGHTGVIAFEVKNTESAKQLIKATSYYTLAESLGAVESLISVPALMTHASIPADIRAKEGITDGLVRISVGIEDTEDLVDDLKQALDTL

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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	226

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8. Citations (1)

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Unit-cell length a length_a	62.832 Å
Unit-cell length b length_b	80.467 Å
Unit-cell length c length_c	161.067 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	8

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	orthorhombic

Resolution resolution	2.330 Å
Low-resolution limit resolution_low	40.270 Å
R factor r_factor	0.2123
R_work r_work	0.2071
R_free r_free	0.2603

fit	/app/data/saxs_computation/xl/9xlu/9xlu.fit
pddf	/app/data/pr_computation/xl/9xlu/9xlu.pr.out
profile	/app/data/saxs_computation/xl/9xlu/9xlu.dat

Crystal structure of Staphylococcus aureus cystathionine gamma-lyase V129G

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

Cystathionine gamma-synthase homolog

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)