SAXSdb — 1t4b

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

Aspartate-semialdehyde dehydrogenase

Escherichia coli

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 1–367 Chain B； UniProt 1–367	Not recorded	NA SODIUM ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；PEG 3350, KCl, Tris.HCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.60 Å R-free 0.199

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 1T4B	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BRM ASPARTATE BETA-SEMIALDEHYDE DEHYDROGENASE FROM ESCHERICHIA COLI Deposited 1998-08-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–367（367 aa） Chain B 1–367（367 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；pH 8.5	Resolution 2.50 Å R-free 0.294
1BRM ASPARTATE BETA-SEMIALDEHYDE DEHYDROGENASE FROM ESCHERICHIA COLI Deposited 1998-08-24	Different construct 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 1–367（367 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；pH 8.5	Resolution 2.50 Å R-free 0.294
1T4D Crystal structure of Escherichia coli aspartate beta-semialdehyde dehydrogenase (EcASADH), at 1.95 Angstrom resolution Deposited 2004-04-29	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–367（367 aa） Chain B 1–367（367 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；PEG 3350, Lithium sulphate, Tris.HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.95 Å R-free 0.250
1T4D Crystal structure of Escherichia coli aspartate beta-semialdehyde dehydrogenase (EcASADH), at 1.95 Angstrom resolution Deposited 2004-04-29	Different construct 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 1–367（367 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；PEG 3350, Lithium sulphate, Tris.HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.95 Å R-free 0.250

2 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DHAS_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–367； UniProt 1–367 Author chain B； PDBConstruct 1–367； UniProt 1–367

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	1t4b
Deposition date deposition_date	2004-04-29
Structure title title	1.6 Angstrom structure of Esherichia coli aspartate-semialdehyde dehydrogenase.
Keywords keywords	;ASADH, aspartate semialdehyde dehydrogenase, HOSR, lysine biosynthesis, NADP+ oxidoreductase (phosphorylating), domain movement, OXIDOREDUCTASE ;; OXIDOREDUCTASE
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	28.76 Å
Radius of gyration Rg (electron density) rg_electron	28.12 Å
Forward intensity I(0) i0	101653000.00
Molecular weight molecular_weight	80135.0 kDa
Excluded volume excluded_volume	100400 Å³
Envelope volume envelope_volume	119880 Å³
Hydration-shell volume shell_volume	36004 Å³
Envelope diameter envelope_diameter	102.9 Å
Shell Rg shell_rg	35.18 Å
Envelope Rg envelope_rg	28.53 Å
Shape Rg shape_rg	28.15 Å
Total Rg total_rg	28.64 Å
Total atoms total_atoms	5625
Residues n_residues	734
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	96.9 Å
Rg (real space) rg_real	28.88 Å
Rg uncertainty (real space) rg_real_error	0.70 Å
I(0) (real space) i0_real	1.0170e+08
I(0) uncertainty (real space) i0_real_error	1.5340e+06
Rg (reciprocal space) rg_reciprocal	28.83 Å
I(0) (reciprocal space) i0_reciprocal	101600000.0000
Solution quality estimate total_estimate	0.8403
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	31.7 Å
Skewness Skewness skewness	0.569
Kurtosis Kurtosis kurtosis	0.064
Angular range angular_range	— – 0.2750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	41480000.0000
Real-space data points n_real_points	56
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.764; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.949; Smooth: 0.681

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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-semialdehyde dehydrogenase
Molecular weight formula_weight	40055.7 kDa
EC 编号 ec_number	1.2.1.11
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	6592

MQNVGFIGWRGMVGSVLMQRMVEERDFDAIRPVFFSTSQLGQAAPSFGGTTGTLQDAFDLEALKALDIIVTCQGGDYTNEIYPKLRESGWQGYWIDAASSLRMKDDAIIILDPVNQDVITDGLNNGIRTFVGGNCTVSLMLMSLGGLFANDLVDWVSVATYQAASGGGARHMRELLTQMGHLYGHVADELATPSSAILDIERKVTTLTRSGELPVDNFGVPLAGSLIPWIDKQLDNGQSREEWKGQAETNKILNTSSVIPVDGLCVRVGALRCHSQAFTIKLKKDVSIPTVEELLAAHNPWAKVVPNDREITMRELTPAAVTGTLTTPVGRLRKLNMGPEFLSAFTVGDQLLWGAAEPLRRMLRQLA

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	967

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1t4ba1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain

Domain ID domain_id	d1t4ba2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.81 — FwdE/GAPDH domain-like
Superfamily Superfamily superfamily	d.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
Family Family family	d.81.1.1 — GAPDH-like

Domain ID domain_id	d1t4bb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain

Domain ID domain_id	d1t4bb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.81 — FwdE/GAPDH domain-like
Superfamily Superfamily superfamily	d.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
Family Family family	d.81.1.1 — GAPDH-like

CATH v4.4 (4 domains)

Domain ID domain_id	1t4bA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	1t4bA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

Domain ID domain_id	1t4bB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	1t4bB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

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8. Citations (1)

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Unit-cell length a length_a	56.500 Å
Unit-cell length b length_b	70.100 Å
Unit-cell length c length_c	180.900 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	1.600 Å
Low-resolution limit resolution_low	29.380 Å
R factor r_factor	0.1700
R_work r_work	0.1700
R_free r_free	0.1990

fit	/app/data/saxs_computation/t4/1t4b/1t4b.fit
pddf	/app/data/pr_computation/t4/1t4b/1t4b.pr.out
profile	/app/data/saxs_computation/t4/1t4b/1t4b.dat

1.6 Angstrom structure of Esherichia coli aspartate-semialdehyde dehydrogenase.

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

Aspartate-semialdehyde dehydrogenase

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