SAXSdb — 5bj3

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

PROTEIN (ASPARTATE AMINOTRANSFERASE)

Thermus aquaticus

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 1–385 Chain B； UniProt 1–385	Mutation：S14D,T16P,K101S,S261R	PLP PYRIDOXAL-5'-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 4.3；CRYSTALLIZED FROM 30MM AMMONIUM PHOSPHATE, PH 4.3	Resolution 2.20 Å R-free 0.243
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–385 Chain D； UniProt 1–385	Mutation：S14D,T16P,K101S,S261R	PLP PYRIDOXAL-5'-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 4.3；CRYSTALLIZED FROM 30MM AMMONIUM PHOSPHATE, PH 4.3	Resolution 2.20 Å R-free 0.243

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 5BJ3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B5O THERMUS THERMOPHILUS ASPARTATE AMINOTRANSFERASE SINGLE MUTANT 1 Deposited 1999-01-07	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 1–385（385 aa） Chain B 1–385（385 aa）	Mutation：K101S Mutation：K101S	PO4 PHOSPHATE ION × 2 PLP PYRIDOXAL-5'-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.3；CRYSTALLIZED FROM 300MM AMMONIUM PHOSPHATE, PH 4.3	Resolution 2.20 Å R-free 0.237
1B5P THERMUS THERMOPHILUS ASPARTATE AMINOTRANSFERASE DOUBLE MUTANT 1 Deposited 1999-01-07	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 1–385（385 aa） Chain B 1–385（385 aa）	Mutation：K101S,S261R Mutation：K101S,S261R	PO4 PHOSPHATE ION × 2 PLP PYRIDOXAL-5'-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.3；CRYSTALLIZED FROM 300MM AMMONIUM PHOSPHATE, PH 4.3	Resolution 1.80 Å R-free 0.239
1BJW ASPARTATE AMINOTRANSFERASE FROM THERMUS THERMOPHILUS Deposited 1998-06-30	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 1–382（382 aa） Chain B 1–382（382 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.3；pH 4.3	Resolution 1.80 Å R-free 0.269
1BKG ASPARTATE AMINOTRANSFERASE FROM THERMUS THERMOPHILUS WITH MALEATE Deposited 1998-07-07	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 1–385（385 aa） Chain B 1–385（385 aa）	Not recorded	PMP 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE × 2 MAE MALEIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 2.60 Å R-free 0.238
1BKG ASPARTATE AMINOTRANSFERASE FROM THERMUS THERMOPHILUS WITH MALEATE Deposited 1998-07-07	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–385（385 aa） Chain D 1–385（385 aa）	Not recorded	PMP 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE × 2 MAE MALEIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 2.60 Å R-free 0.238
1GC3 THERMUS THERMOPHILUS ASPARTATE AMINOTRANSFERASE TETRA MUTANT 2 COMPLEXED WITH TRYPTOPHAN Deposited 2000-07-18	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 1–385（385 aa） Chain B 1–385（385 aa）	Mutation：S14D, T16V, K101S, S261R Mutation：S14D, T16V, K101S, S261R	TRP TRYPTOPHAN × 2 PLP PYRIDOXAL-5'-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；PEG 6000, HEPES, sodium acetate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.30 Å R-free 0.282
1GC3 THERMUS THERMOPHILUS ASPARTATE AMINOTRANSFERASE TETRA MUTANT 2 COMPLEXED WITH TRYPTOPHAN Deposited 2000-07-18	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–385（385 aa） Chain D 1–385（385 aa）	Mutation：S14D, T16V, K101S, S261R Mutation：S14D, T16V, K101S, S261R	TRP TRYPTOPHAN × 2 PLP PYRIDOXAL-5'-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；PEG 6000, HEPES, sodium acetate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.30 Å R-free 0.282
1GC3 THERMUS THERMOPHILUS ASPARTATE AMINOTRANSFERASE TETRA MUTANT 2 COMPLEXED WITH TRYPTOPHAN Deposited 2000-07-18	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 1–385（385 aa） Chain F 1–385（385 aa）	Mutation：S14D, T16V, K101S, S261R Mutation：S14D, T16V, K101S, S261R	TRP TRYPTOPHAN × 2 PLP PYRIDOXAL-5'-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；PEG 6000, HEPES, sodium acetate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.30 Å R-free 0.282
1GC3 THERMUS THERMOPHILUS ASPARTATE AMINOTRANSFERASE TETRA MUTANT 2 COMPLEXED WITH TRYPTOPHAN Deposited 2000-07-18	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain G 1–385（385 aa） Chain H 1–385（385 aa）	Mutation：S14D, T16V, K101S, S261R Mutation：S14D, T16V, K101S, S261R	TRP TRYPTOPHAN × 2 PLP PYRIDOXAL-5'-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；PEG 6000, HEPES, sodium acetate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.30 Å R-free 0.282
1GC4 THERMUS THERMOPHILUS ASPARTATE AMINOTRANSFERASE TETRA MUTANT 2 COMPLEXED WITH ASPARTATE Deposited 2000-07-19	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 1–385（385 aa） Chain B 1–385（385 aa）	Mutation：S14D, T16V, K101S, S261R Mutation：S14D, T16V, K101S, S261R	ASP ASPARTIC ACID × 2 PLP PYRIDOXAL-5'-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；PEG 6000, HEPES, sodium acetate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.30 Å R-free 0.277
1GC4 THERMUS THERMOPHILUS ASPARTATE AMINOTRANSFERASE TETRA MUTANT 2 COMPLEXED WITH ASPARTATE Deposited 2000-07-19	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–385（385 aa） Chain D 1–385（385 aa）	Mutation：S14D, T16V, K101S, S261R Mutation：S14D, T16V, K101S, S261R	ASP ASPARTIC ACID × 2 PLP PYRIDOXAL-5'-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；PEG 6000, HEPES, sodium acetate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.30 Å R-free 0.277
1GCK THERMUS THERMOPHILUS ASPARTATE AMINOTRANSFERASE DOUBLE MUTANT 1 COMPLEXED WITH ASPARTATE Deposited 2000-08-04	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 1–385（385 aa） Chain B 1–385（385 aa）	Mutation：K101S, S261R Mutation：K101S, S261R	ASP ASPARTIC ACID × 2 PLP PYRIDOXAL-5'-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；PEG 6000, HEPES, sodium acetate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.284
5BJ4 THERMUS THERMOPHILUS ASPARTATE AMINOTRANSFERASE TETRA MUTANT 2 Deposited 1999-01-11	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 1–385（385 aa） Chain B 1–385（385 aa）	Mutation：S14D,T16V,K101S,S261R Mutation：S14D,T16V,K101S,S261R	PO4 PHOSPHATE ION × 2 PLP PYRIDOXAL-5'-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.3；CRYSTALLIZED FROM 300MM AMMONIUM PHOSPHATE, PH 4.3	Resolution 2.00 Å R-free 0.214

8 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	AAT_THET8
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–385； UniProt 1–385 Author chain B； PDBConstruct 1–385； UniProt 1–385 Author chain C； PDBConstruct 1–385； UniProt 1–385 Author chain D； PDBConstruct 1–385； UniProt 1–385

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	5bj3
Deposition date deposition_date	1999-01-11
Structure title title	THERMUS THERMOPHILUS ASPARTATE AMINOTRANSFERASE TETRA MUTANT 1
Keywords keywords	AMINOTRANSFERASE, PYRIDOXAL ENZYME, 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	43.34 Å
Radius of gyration Rg (electron density) rg_electron	43.65 Å
Forward intensity I(0) i0	376404000.00
Molecular weight molecular_weight	160090.0 kDa
Excluded volume excluded_volume	200880 Å³
Envelope volume envelope_volume	256500 Å³
Hydration-shell volume shell_volume	51653 Å³
Envelope diameter envelope_diameter	152.2 Å
Shell Rg shell_rg	44.84 Å
Envelope Rg envelope_rg	43.52 Å
Shape Rg shape_rg	43.64 Å
Total Rg total_rg	43.72 Å
Total atoms total_atoms	11288
Residues n_residues	1452
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	154.8 Å
Rg (real space) rg_real	43.76 Å
Rg uncertainty (real space) rg_real_error	1.91 Å
I(0) (real space) i0_real	3.7640e+08
I(0) uncertainty (real space) i0_real_error	7.4570e+06
Rg (reciprocal space) rg_reciprocal	43.34 Å
I(0) (reciprocal space) i0_reciprocal	376200000.0000
Solution quality estimate total_estimate	0.7977
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	38.7 Å
Skewness Skewness skewness	0.546
Kurtosis Kurtosis kurtosis	-0.380
Angular range angular_range	— – 0.1800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	54240000.0000
Real-space data points n_real_points	37
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.644; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.654; Smooth: 0.781

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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	PROTEIN (ASPARTATE AMINOTRANSFERASE)
Molecular weight formula_weight	42155.0 kDa
EC 编号 ec_number	2.6.1.1
Mutation mutation	S14D,T16P,K101S,S261R
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	11621

MRGLSRRVQAMKPDAPVAVNAKALELRRQGVDLVALTAGEPDFDTPEHVKEAARRALAQGKTKYAPPAGIPELREALAEKFRRENGLSVTPEETIVTVGGSQALFNLFQAILDPGDEVIVLSPYWVSYPEMVRFAGGVVVEVETLPEEGFVPDPERVRRAITPRTKALVVNSPNNPTGAVYPKEVLEALARLAVEHDFYLVSDEIYEHLLYEGEHFSPGRVAPEHTLTVNGAAKAFAMTGWRIGYACGPKEVIKAMASVSRQSTTSPDTIAQWATLEALTNQEASRAFVEMAREAYRRRRDLLLEGLTALGLKAVRPSGAFYVLMDTSPIAPDEVRAAERLLEAGVAVVPGTDFAAFGHVRLSYATSEENLRKALERFARVLGRA

来源 Source

来源生物 organism	Thermus aquaticus
NCBI Class编号 ncbi_taxonomy_id	271
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	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	333

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d5bj3a_
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	d5bj3b_
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	d5bj3c_
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	d5bj3d_
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 (8 domains)

Domain ID domain_id	5bj3A01
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	5bj3A02
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	5bj3B01
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	5bj3B02
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	5bj3C01
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	5bj3C02
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	5bj3D01
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	5bj3D02
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 (1)

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Unit-cell length a length_a	106.440 Å
Unit-cell length b length_b	62.250 Å
Unit-cell length c length_c	154.770 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	109.07 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.2150
R_work r_work	0.2150
R_free r_free	0.2430

fit	/app/data/saxs_computation/bj/5bj3/5bj3.fit
pddf	/app/data/pr_computation/bj/5bj3/5bj3.pr.out
profile	/app/data/saxs_computation/bj/5bj3/5bj3.dat

THERMUS THERMOPHILUS ASPARTATE AMINOTRANSFERASE TETRA MUTANT 1

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

PROTEIN (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