SAXSdb — 1w3u

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

PHOSPHOSERINE AMINOTRANSFERASE

BACILLUS CIRCULANS

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 1–362	Mutation：YES	PLP PYRIDOXAL-5'-PHOSPHATE × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 4.6；CRYSTALLIZED AT ROOM TEMPERATURE FROM 0.1 M SODIUM ACETATE BUFFER, PH 4.6, 5% GLYCEROL, 4% PEG 20000	Resolution 1.50 Å R-free 0.208

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 1W3U	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BT4 PHOSPHOSERINE AMINOTRANSFERASE FROM BACILLUS CIRCULANS SUBSP. ALKALOPHILUS Deposited 1998-09-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 4–362（359 aa） Fragment：ONE COMPLETE SUBUNIT	Mutation：K3E	PLP PYRIDOXAL-5'-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions macroseeding；pH 4.6；CRYSTALLIZED AT ROOM TEMPERATURE FROM 0.1 M SODIUM ACETATE BUFFER, PH 4.6, 2-6% GLYCEROL, 2-4% PEG 20000, USING MACROSEEDING TECHNIQUES, macroseeding	Resolution 2.30 Å R-free 0.246
2C0R CRYSTAL STRUCTURE OF PHOSPHOSERINE AMINOTRANSFERASE FROM BACILLUS CIRCULANS VAR. ALKALOPHILUS AT pH 8.5 Deposited 2005-09-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–361（361 aa） Chain B 1–361（361 aa）	Mutation：YES Mutation：YES	PLP PYRIDOXAL-5'-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；30% PEG 4000, 0.1 M TRIS-HCL BUFFER, PH 8.5, 5% GLYCEROL, 0.2 M SODIUM ACETATE	Resolution 1.20 Å R-free 0.212

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SERC_BACCI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–362； UniProt 1–362

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	1w3u
Deposition date deposition_date	2004-07-20
Structure title title	Crystal structure of phosphoserine aminotransferase from Bacillus circulans var. alkalophilus
Keywords keywords	;TRANSFERASE, PHOSPHOSERINE AMINOTRANSFERASE, PYRIDOXAL-5'-PHOSPHATE TRANSFERASE, PYRIDINE SERINE BIOSYNTHESIS ;; TRANSFERASE
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	22.04 Å
Radius of gyration Rg (electron density) rg_electron	20.90 Å
Forward intensity I(0) i0	27103200.00
Molecular weight molecular_weight	39585.0 kDa
Excluded volume excluded_volume	49355 Å³
Envelope volume envelope_volume	56626 Å³
Hydration-shell volume shell_volume	22575 Å³
Envelope diameter envelope_diameter	72.7 Å
Shell Rg shell_rg	27.61 Å
Envelope Rg envelope_rg	21.25 Å
Shape Rg shape_rg	20.90 Å
Total Rg total_rg	21.73 Å
Total atoms total_atoms	2785
Residues n_residues	360
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	69.7 Å
Rg (real space) rg_real	21.97 Å
Rg uncertainty (real space) rg_real_error	0.45 Å
I(0) (real space) i0_real	2.7100e+07
I(0) uncertainty (real space) i0_real_error	3.4040e+05
Rg (reciprocal space) rg_reciprocal	21.99 Å
I(0) (reciprocal space) i0_reciprocal	27100000.0000
Solution quality estimate total_estimate	0.8253
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.0 Å
Skewness Skewness skewness	0.267
Kurtosis Kurtosis kurtosis	-0.464
Angular range angular_range	— – 0.3600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6928000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.910; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000

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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	PHOSPHOSERINE AMINOTRANSFERASE
Molecular weight formula_weight	39966.1 kDa
EC 编号 ec_number	2.6.1.52
Mutation mutation	YES
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	3132

MSERAYNFNAGPAALPLEVLERAQAEFVDYQHTGMSIMEMSHRGAVYEAVHNEAQARLLALLGNPTGYKVLFIQGGASTQFAMIPMNFLKEGQTANYVMTGSWASKALKEAKLIGDTHVAASSEASNYMTLPKLQEIQLQDNAAYLHLTSNETIEGAQFKAFPDTGSVPLIGDMSSDILSRPFDLNQFGLVYAGAQKNLGPSGVTVVIVREDLVAESPKHLPTMLRYDTYVKNNSLYNTPPSFGIYMVNEVLKWIEERGGLEGVQQANRKKASLIYDAIDQSGGFYRGCVDVDSRSDMNITFRLASEELEKEFVKASEQEGFVGLKGHRSVGGLRASIYNAVPYESCEALVQFMEHFKRSRG

来源 Source

来源生物 organism	BACILLUS CIRCULANS
NCBI Class编号 ncbi_taxonomy_id	1397
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	PYRIDOXAL-5'-PHOSPHATE
Molecular weight formula_weight	247.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	340

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1w3ua_
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.67.1.4 — GABA-aminotransferase-like

CATH v4.4 (2 domains)

Domain ID domain_id	1w3uA01
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	1w3uA02
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	91.287 Å
Unit-cell length b length_b	91.109 Å
Unit-cell length c length_c	42.374 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	111.25 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.500 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.1421
R_work r_work	—
R_free r_free	0.2080

fit	/app/data/saxs_computation/w3/1w3u/1w3u.fit
pddf	/app/data/pr_computation/w3/1w3u/1w3u.pr.out
profile	/app/data/saxs_computation/w3/1w3u/1w3u.dat

Crystal structure of phosphoserine aminotransferase from Bacillus circulans var. alkalophilus

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

PHOSPHOSERINE AMINOTRANSFERASE

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