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9j7p

Crystal structure of S. aureus MccB mutant S323A

Method: X-RAY DIFFRACTION Dmax: 70.1 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Cystathionine gamma-synthase homolog

Staphylococcus aureus subsp. aureus Mu50

UniProt A0A0H3JQ19

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：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

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 9J7P 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 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
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 2–381； 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.

SAXS scattering curve SAXS Profile

SAXS profile for 9j7p

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9j7p
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9j7p
Deposition date deposition_date2024-08-19
最后修订 last_revision2025-09-03
Structure title titleCrystal structure of S. aureus MccB mutant S323A
Keywords keywordsCGL, PLP, MccB, LYASE; LYASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier21.73 Å
Radius of gyration Rg (electron density) rg_electron20.70 Å
Forward intensity I(0) i026104400.00
Molecular weight molecular_weight39435.0 kDa
Excluded volume excluded_volume49570 ų
Envelope volume envelope_volume58043 ų
Hydration-shell volume shell_volume23207 ų
Envelope diameter envelope_diameter74.7 Å
Shell Rg shell_rg27.64 Å
Envelope Rg envelope_rg21.08 Å
Shape Rg shape_rg20.70 Å
Total Rg total_rg21.57 Å
Total atoms total_atoms2774
Residues n_residues364
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax70.1 Å
Rg (real space) rg_real21.63 Å
Rg uncertainty (real space) rg_real_error0.37 Å
I(0) (real space) i0_real2.6100e+07
I(0) uncertainty (real space) i0_real_error3.5280e+05
Rg (reciprocal space) rg_reciprocal21.65 Å
I(0) (reciprocal space) i0_reciprocal26100000.0000
Solution quality estimate total_estimate0.8900
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary69.0 Å
Skewness Skewness skewness0.226
Kurtosis Kurtosis kurtosis-0.411
Angular range angular_range— – 0.3650 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6153000.0000
Real-space data points n_real_points68
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.871; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.954
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)