SAXSdb — 1d6s

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

O-ACETYLSERINE SULFHYDRYLASE

Salmonella typhimurium

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–322 Chain B； UniProt 1–322	Mutation：K41A	MET METHIONINE × 2 PLP PYRIDOXAL-5'-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；297 K；30 % PEG 4000 8 % ETHANOL 100 MM TRIS (PH 7.0) 150 MM LI2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 2.30 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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	CYSK_SALTY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–322； UniProt 1–322 Author chain B； PDBConstruct 1–322； UniProt 1–322

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	1d6s
Deposition date deposition_date	1999-10-15
Structure title title	CRYSTAL STRUCTURE OF THE K41A MUTANT OF O-ACETYLSERINE SULFHYDRYLASE COMPLEXED IN EXTERNAL ALDIMINE LINKAGE WITH METHIONINE
Keywords keywords	CYSTEINE BIOSYNTHESIS, BETA REPLACEMENT ENZYME, PLP, K41A, 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	25.35 Å
Radius of gyration Rg (electron density) rg_electron	24.36 Å
Forward intensity I(0) i0	76812200.00
Molecular weight molecular_weight	69502.0 kDa
Excluded volume excluded_volume	87562 Å³
Envelope volume envelope_volume	101250 Å³
Hydration-shell volume shell_volume	33414 Å³
Envelope diameter envelope_diameter	86.1 Å
Shell Rg shell_rg	32.73 Å
Envelope Rg envelope_rg	24.62 Å
Shape Rg shape_rg	24.37 Å
Total Rg total_rg	25.20 Å
Total atoms total_atoms	4882
Residues n_residues	644
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	83.0 Å
Rg (real space) rg_real	25.24 Å
Rg uncertainty (real space) rg_real_error	0.42 Å
I(0) (real space) i0_real	7.6810e+07
I(0) uncertainty (real space) i0_real_error	1.0580e+06
Rg (reciprocal space) rg_reciprocal	25.28 Å
I(0) (reciprocal space) i0_reciprocal	76810000.0000
Solution quality estimate total_estimate	0.8849
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.3 Å
Skewness Skewness skewness	0.232
Kurtosis Kurtosis kurtosis	-0.374
Angular range angular_range	— – 0.3150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	24120000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.840; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.980

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	O-ACETYLSERINE SULFHYDRYLASE
Molecular weight formula_weight	34412.3 kDa
EC 编号 ec_number	4.2.99.8
Mutation mutation	K41A
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5115

SKIYEDNSLTIGHTPLVRLNRIGNGRILAKVESRNPSFSVACRIGANMIWDAEKRGVLKPGVELVEPTNGNTGIALAYVAAARGYKLTLTMPETMSIERRKLLKALGANLVLTEGAKGMKGAIQKAEEIVASDPQKYLLLQQFSNPANPEIHEKTTGPEIWEDTDGQVDVFISGVGTGGTLTGVTRYIKGTKGKTDLITVAVEPTDSPVIAQALAGEEIKPGPHKIQGIGAGFIPGNLDLKLIDKVVGITNEEAISTARRLMEEEGILAGISSGAAVAAALKLQEDESFTNKNIVVILPSSGERYLSTALFADLFTEKELQQ

来源 Source

来源生物 organism	Salmonella typhimurium
NCBI Class编号 ncbi_taxonomy_id	602
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	METHIONINE
Molecular weight formula_weight	149.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	PYRIDOXAL-5'-PHOSPHATE
Molecular weight formula_weight	247.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	233

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1d6sa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.79 — Tryptophan synthase beta subunit-like PLP-dependent enzymes
Superfamily Superfamily superfamily	c.79.1 — Tryptophan synthase beta subunit-like PLP-dependent enzymes
Family Family family	c.79.1.1 — Tryptophan synthase beta subunit-like PLP-dependent enzymes

Domain ID domain_id	d1d6sb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.79 — Tryptophan synthase beta subunit-like PLP-dependent enzymes
Superfamily Superfamily superfamily	c.79.1 — Tryptophan synthase beta subunit-like PLP-dependent enzymes
Family Family family	c.79.1.1 — Tryptophan synthase beta subunit-like PLP-dependent enzymes

CATH v4.4 (4 domains)

Domain ID domain_id	1d6sA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1100 —

Domain ID domain_id	1d6sA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1100 —

Domain ID domain_id	1d6sB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1100 —

Domain ID domain_id	1d6sB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1100 —

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8. Citations (2)

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Unit-cell length a length_a	96.940 Å
Unit-cell length b length_b	149.930 Å
Unit-cell length c length_c	53.640 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	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	29.670 Å
R factor r_factor	0.1740
R_work r_work	0.1740
R_free r_free	0.2230

fit	/app/data/saxs_computation/d6/1d6s/1d6s.fit
pddf	/app/data/pr_computation/d6/1d6s/1d6s.pr.out
profile	/app/data/saxs_computation/d6/1d6s/1d6s.dat

CRYSTAL STRUCTURE OF THE K41A MUTANT OF O-ACETYLSERINE SULFHYDRYLASE COMPLEXED IN EXTERNAL ALDIMINE LINKAGE WITH METHIONINE

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

O-ACETYLSERINE SULFHYDRYLASE

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