1b26

GLUTAMATE DEHYDROGENASE

Method: X-RAY DIFFRACTION D_max: 135.1 Å Quality: GOOD

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

GLUTAMATE DEHYDROGENASE

Thermotoga maritima

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 1–416 Chain B； UniProt 1–416 Chain C； UniProt 1–416 Chain D； UniProt 1–416 Chain E； UniProt 1–416 Chain F； UniProt 1–416	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；CRYSTALLIZATION CONDITIONS: 3% POLYETHYLENE GLYCOLE, 120 MM AMMONIUM ACETATE 50 MM BIS-TRIS PROPANE PH 6.5	Resolution 3.00 Å R-free 0.295

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 1B26	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B3B THERMOTOGA MARITIMA GLUTAMATE DEHYDROGENASE MUTANT N97D, G376K Deposited 1998-12-07	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 2–416（415 aa） Chain B 2–416（415 aa） Chain C 2–416（415 aa） Chain D 2–416（415 aa） Chain E 2–416（415 aa） Chain F 2–416（415 aa）	Mutation：N97D, G376K Mutation：N97D, G376K Mutation：N97D, G376K Mutation：N97D, G376K Mutation：N97D, G376K Mutation：N97D, G376K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；6% POLYETHYLENE GLYCOLE, 120 MM AMMONIUM ACETATE, 50 MM BIS-TRIS PROPANE PH 6.5	Resolution 3.10 Å R-free 0.298
2TMG THERMOTOGA MARITIMA GLUTAMATE DEHYDROGENASE MUTANT S128R, T158E, N117R, S160E Deposited 1998-12-04	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 2–416（415 aa） Chain B 2–416（415 aa） Chain C 2–416（415 aa） Chain D 2–416（415 aa） Chain E 2–416（415 aa） Chain F 2–416（415 aa）	Mutation：S128R, T158E, N117R, S160E Mutation：S128R, T158E, N117R, S160E Mutation：S128R, T158E, N117R, S160E Mutation：S128R, T158E, N117R, S160E Mutation：S128R, T158E, N117R, S160E Mutation：S128R, T158E, N117R, S160E	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；6% POLYETHYLENE GLYCOLE, 120 MM AMMONIUM ACETATE, 50 MM BIS-TRIS PROPANE PH 6.5	Resolution 2.90 Å R-free 0.274

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

View Construct and Data Evidence

UniProt name	DHE3_THEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–416； UniProt 1–416 Author chain B； PDBConstruct 1–416； UniProt 1–416 Author chain C； PDBConstruct 1–416； UniProt 1–416 Author chain D； PDBConstruct 1–416； UniProt 1–416 Author chain E； PDBConstruct 1–416； UniProt 1–416 Author chain F； PDBConstruct 1–416； UniProt 1–416

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1b26
Deposition date deposition_date	1998-12-04
Structure title title	GLUTAMATE DEHYDROGENASE
Keywords keywords	METABOLIC ROLE, GLUTAMATE, DEHYDROGENASE, 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	42.51 Å
Radius of gyration Rg (electron density) rg_electron	41.86 Å
Forward intensity I(0) i0	1046780000.00
Molecular weight molecular_weight	269530.0 kDa
Excluded volume excluded_volume	338880 Å³
Envelope volume envelope_volume	438320 Å³
Hydration-shell volume shell_volume	84155 Å³
Envelope diameter envelope_diameter	139.7 Å
Shell Rg shell_rg	48.86 Å
Envelope Rg envelope_rg	41.77 Å
Shape Rg shape_rg	41.83 Å
Total Rg total_rg	42.30 Å
Total atoms total_atoms	18978
Residues n_residues	2454
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	135.1 Å
Rg (real space) rg_real	42.31 Å
Rg uncertainty (real space) rg_real_error	1.12 Å
I(0) (real space) i0_real	1.0470e+09
I(0) uncertainty (real space) i0_real_error	1.9100e+07
Rg (reciprocal space) rg_reciprocal	42.50 Å
I(0) (reciprocal space) i0_reciprocal	1047000000.0000
Solution quality estimate total_estimate	0.8785
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	54.8 Å
Skewness Skewness skewness	0.194
Kurtosis Kurtosis kurtosis	-0.351
Angular range angular_range	— – 0.1850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	152700000.0000
Real-space data points n_real_points	38
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.874; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.822

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d1b26a1
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.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain

Domain ID domain_id	d1b26a2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.58 — Aminoacid dehydrogenase-like, N-terminal domain
Superfamily Superfamily superfamily	c.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
Family Family family	c.58.1.1 — Aminoacid dehydrogenases

Domain ID domain_id	d1b26b1
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.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain

Domain ID domain_id	d1b26b2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.58 — Aminoacid dehydrogenase-like, N-terminal domain
Superfamily Superfamily superfamily	c.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
Family Family family	c.58.1.1 — Aminoacid dehydrogenases

Domain ID domain_id	d1b26c1
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.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain

Domain ID domain_id	d1b26c2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.58 — Aminoacid dehydrogenase-like, N-terminal domain
Superfamily Superfamily superfamily	c.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
Family Family family	c.58.1.1 — Aminoacid dehydrogenases

Domain ID domain_id	d1b26d1
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.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain

Domain ID domain_id	d1b26d2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.58 — Aminoacid dehydrogenase-like, N-terminal domain
Superfamily Superfamily superfamily	c.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
Family Family family	c.58.1.1 — Aminoacid dehydrogenases

Domain ID domain_id	d1b26e1
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.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain

Domain ID domain_id	d1b26e2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.58 — Aminoacid dehydrogenase-like, N-terminal domain
Superfamily Superfamily superfamily	c.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
Family Family family	c.58.1.1 — Aminoacid dehydrogenases

Domain ID domain_id	d1b26f1
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.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain

Domain ID domain_id	d1b26f2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.58 — Aminoacid dehydrogenase-like, N-terminal domain
Superfamily Superfamily superfamily	c.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
Family Family family	c.58.1.1 — Aminoacid dehydrogenases

CATH v4.4 (12 domains)

Domain ID domain_id	1b26A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10860 — Leucine Dehydrogenase, chain A, domain 1

Domain ID domain_id	1b26A02
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	1b26B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10860 — Leucine Dehydrogenase, chain A, domain 1

Domain ID domain_id	1b26B02
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	1b26C01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10860 — Leucine Dehydrogenase, chain A, domain 1

Domain ID domain_id	1b26C02
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	1b26D01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10860 — Leucine Dehydrogenase, chain A, domain 1

Domain ID domain_id	1b26D02
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	1b26E01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10860 — Leucine Dehydrogenase, chain A, domain 1

Domain ID domain_id	1b26E02
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	1b26F01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10860 — Leucine Dehydrogenase, chain A, domain 1

Domain ID domain_id	1b26F02
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

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8. Citations (1)

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Unit-cell length a length_a	147.130 Å
Unit-cell length b length_b	147.130 Å
Unit-cell length c length_c	273.640 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	36

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	—
R_work r_work	0.2250
R_free r_free	0.2950

Description description	GLUTAMATE DEHYDROGENASE
Molecular weight formula_weight	45859.5 kDa
EC 编号 ec_number	1.4.1.3
Source method src_method	man
Copy count entity_count	6

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	18978

GLUTAMATE DEHYDROGENASE

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

GLUTAMATE 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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Thermotoga maritima
NCBI Class编号 ncbi_taxonomy_id	2336
宿主生物 host_organism	Escherichia coli BL21(DE3)

fit	/app/data/saxs_computation/b2/1b26/1b26.fit
pddf	/app/data/pr_computation/b2/1b26/1b26.pr.out
profile	/app/data/saxs_computation/b2/1b26/1b26.dat