SAXSdb — 1gd9

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

ASPARTATE AMINOTRANSFERASE

Pyrococcus horikoshii

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 1–389 Chain B； UniProt 1–389	Not recorded	PLP PYRIDOXAL-5'-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；1,6-hexane diol, Tris, magnesium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 1.80 Å R-free 0.242

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 1GD9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DJU CRYSTAL STRUCTURE OF AROMATIC AMINOTRANSFERASE FROM PYROCOCCUS HORIKOSHII OT3 Deposited 1999-12-06	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–389（388 aa） Chain B 2–389（388 aa）	Not recorded	PLP PYRIDOXAL-5'-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；1,6-HEXANE-DI-OL, MAGNESIUM CHLORIDE, PYRIDOXAL-5'-PHOSPHATE, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.10 Å R-free 0.254

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	O59096_PYRHO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–389； UniProt 1–389 Author chain B； PDBConstruct 1–389； UniProt 1–389

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	1gd9
Deposition date deposition_date	2000-09-22
Structure title title	CRYSTALL STRUCTURE OF PYROCOCCUS PROTEIN-A1
Keywords keywords	aminotransferase, pyridoxal enzyme, temperature dependence of substrate recognition, TRANSFERASE; 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	28.45 Å
Radius of gyration Rg (electron density) rg_electron	27.44 Å
Forward intensity I(0) i0	114650000.00
Molecular weight molecular_weight	87994.0 kDa
Excluded volume excluded_volume	111520 Å³
Envelope volume envelope_volume	126200 Å³
Hydration-shell volume shell_volume	37793 Å³
Envelope diameter envelope_diameter	104.3 Å
Shell Rg shell_rg	35.69 Å
Envelope Rg envelope_rg	27.59 Å
Shape Rg shape_rg	27.42 Å
Total Rg total_rg	28.28 Å
Total atoms total_atoms	6194
Residues n_residues	776
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	94.0 Å
Rg (real space) rg_real	28.43 Å
Rg uncertainty (real space) rg_real_error	0.73 Å
I(0) (real space) i0_real	1.1470e+08
I(0) uncertainty (real space) i0_real_error	1.6120e+06
Rg (reciprocal space) rg_reciprocal	28.44 Å
I(0) (reciprocal space) i0_reciprocal	114700000.0000
Solution quality estimate total_estimate	0.8048
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	35.2 Å
Skewness Skewness skewness	0.374
Kurtosis Kurtosis kurtosis	-0.235
Angular range angular_range	— – 0.2800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	61410000.0000
Real-space data points n_real_points	57
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.822; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; 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	ASPARTATE AMINOTRANSFERASE
Molecular weight formula_weight	43960.8 kDa
EC 编号 ec_number	2.6.1.-
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	6666

MALSDRLELVSASEIRKLFDIAAGMKDVISLGIGEPDFDTPQHIKEYAKEALDKGLTHYGPNIGLLELREAIAEKLKKQNGIEADPKTEIMVLLGANQAFLMGLSAFLKDGEEVLIPTPAFVSYAPAVILAGGKPVEVPTYEEDEFRLNVDELKKYVTDKTRALIINSPCNPTGAVLTKKDLEEIADFVVEHDLIVISDEVYEHFIYDDARHYSIASLDGMFERTITVNGFSKTFAMTGWRLGFVAAPSWIIERMVKFQMYNATCPVTFIQYAAAKALKDERSWKAVEEMRKEYDRRRKLVWKRLNEMGLPTVKPKGAFYIFPRIRDTGLTSKKFSELMLKEARVAVVPGSAFGKAGEGYVRISYATAYEKLEEAMDRMERVLKERKLV

来源 Source

来源生物 organism	Pyrococcus horikoshii
NCBI Class编号 ncbi_taxonomy_id	53953
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	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	472

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1gd9a_
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.67.1.1 — AAT-like

Domain ID domain_id	d1gd9b_
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.67.1.1 — AAT-like

CATH v4.4 (4 domains)

Domain ID domain_id	1gd9A01
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

Domain ID domain_id	1gd9A02
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	1gd9B01
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

Domain ID domain_id	1gd9B02
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)

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8. Citations (2)

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Unit-cell length a length_a	59.670 Å
Unit-cell length b length_b	122.280 Å
Unit-cell length c length_c	127.170 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 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.2120
R_work r_work	0.2100
R_free r_free	0.2420

fit	/app/data/saxs_computation/gd/1gd9/1gd9.fit
pddf	/app/data/pr_computation/gd/1gd9/1gd9.pr.out
profile	/app/data/saxs_computation/gd/1gd9/1gd9.dat

CRYSTALL STRUCTURE OF PYROCOCCUS PROTEIN-A1

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

ASPARTATE 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