SAXSdb — 1bgv

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

GLUTAMATE DEHYDROGENASE

OrganismNot specified

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 1–449	Not recorded	GLU GLUTAMIC ACID × 6	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；pH 7.0	Resolution 1.90 Å

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 1BGV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AUP GLUTAMATE DEHYDROGENASE Deposited 1997-09-01	Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–449（449 aa）	Mutation：K89L, S380V	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.0	Resolution 2.50 Å
1HRD GLUTAMATE DEHYDROGENASE Deposited 1996-04-03	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–449（449 aa） Chain B 1–449（449 aa） Chain C 1–449（449 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.96 Å
1K89 K89L MUTANT OF GLUTAMATE DEHYDROGENASE Deposited 1998-06-05	Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–449（449 aa）	Mutation：K89L	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.0	Resolution 2.05 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DHE2_CLOSY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–449； UniProt 1–449

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	1bgv
Deposition date deposition_date	1998-06-01
Structure title title	GLUTAMATE DEHYDROGENASE
Keywords keywords	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	22.84 Å
Radius of gyration Rg (electron density) rg_electron	21.79 Å
Forward intensity I(0) i0	40465700.00
Molecular weight molecular_weight	49298.0 kDa
Excluded volume excluded_volume	61660 Å³
Envelope volume envelope_volume	71145 Å³
Hydration-shell volume shell_volume	26584 Å³
Envelope diameter envelope_diameter	69.3 Å
Shell Rg shell_rg	29.18 Å
Envelope Rg envelope_rg	21.87 Å
Shape Rg shape_rg	21.81 Å
Total Rg total_rg	22.60 Å
Total atoms total_atoms	3470
Residues n_residues	449
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	69.1 Å
Rg (real space) rg_real	22.70 Å
Rg uncertainty (real space) rg_real_error	0.29 Å
I(0) (real space) i0_real	4.0470e+07
I(0) uncertainty (real space) i0_real_error	5.6270e+05
Rg (reciprocal space) rg_reciprocal	22.73 Å
I(0) (reciprocal space) i0_reciprocal	40470000.0000
Solution quality estimate total_estimate	0.9083
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.3 Å
Skewness Skewness skewness	0.109
Kurtosis Kurtosis kurtosis	-0.516
Angular range angular_range	— – 0.3500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9628000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.946; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.982

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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	GLUTAMATE DEHYDROGENASE
Molecular weight formula_weight	49215.6 kDa
EC 编号 ec_number	1.4.1.2
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3687

SKYVDRVIAEVEKKYADEPEFVQTVEEVLSSLGPVVDAHPEYEEVALLERMVIPERVIEFRVPWEDDNGKVHVNTGYRVQFNGAIGPYKGGLRFAPSVNLSIMKFLGFEQAFKDSLTTLPMGGAKGGSDFDPNGKSDREVMRFCQAFMTELYRHIGPDIDVPAGDLGVGAREIGYMYGQYRKIVGGFYNGVLTGKARSFGGSLVRPEATGYGSVYYVEAVMKHENDTLVGKTVALAGFGNVAWGAAKKLAELGAKAVTLSGPDGYIYDPEGITTEEKINYMLEMRASGRNKVQDYADKFGVQFFPGEKPWGQKVDIIMPCATQNDVDLEQAKKIVANNVKYYIEVANMPTTNEALRFLMQQPNMVVAPSKAVNAGGVLVSGFEMSQNSERLSWTAEEVDSKLHQVMTDIHDGSAAAAERYGLGYNLVAGANIVGFQKIADAMMAQGIAW

Entity 2 Entity 2 non-polymer

Description description	GLUTAMIC ACID
Molecular weight formula_weight	147.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	217

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1bgva1
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	d1bgva2
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 (3 domains)

Domain ID domain_id	1bgvA01
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	1bgvA02
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	1bgvA03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	285 — Glutamate Dehydrogenase; Chain A, domain 3
Homologous superfamily homologous superfamily	10 — Glutamate Dehydrogenase, chain A, domain 3

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8. Citations (8)

Conformational flexibility in glutamate dehydrogenase. Role of water in substrate recognition and catalysis.

J.Mol.Biol. (1993)

PMID: 8263917 · DOI: 10.1006/jmbi.1993.1665 PRIMARY

Determinants of Substrate Specificity in the Superfamily of Amino Acid Dehydrogenases

Biochemistry (1997)

;The Structure of Pyrococcus Furiosus Glutamate Dehydrogenase Reveals a Key Role for Ion-Pair Networks in Maintaining Enzyme Stability at Extreme Temperatures ;

Structure (1995)

;Erratum. Structural Consequences of Sequence Patterns in the Fingerprint Region of the Nucleotide Binding Fold. Implications for Nucleotide Specificity ;

J.Mol.Biol. (1993)

;Structural Consequences of Sequence Patterns in the Fingerprint Region of the Nucleotide Binding Fold. Implications for Nucleotide Specificity ;

J.Mol.Biol. (1992)

Subunit Assembly and Active Site Location in the Structure of Glutamate Dehydrogenase

Proteins (1992)

Structural Relationship between the Hexameric and Tetrameric Family of Glutamate Dehydrogenases

Eur.J.Biochem. (1992)

Crystallization of an Nad+-Dependent Glutamate Dehydrogenase from Clostridium Symbiosum

J.Mol.Biol. (1985)

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Unit-cell length a length_a	162.800 Å
Unit-cell length b length_b	162.800 Å
Unit-cell length c length_c	102.800 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	18

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	—
R_work r_work	0.1730
R_free r_free	—

fit	/app/data/saxs_computation/bg/1bgv/1bgv.fit
pddf	/app/data/pr_computation/bg/1bgv/1bgv.pr.out
profile	/app/data/saxs_computation/bg/1bgv/1bgv.dat

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

8. Citations (8)

9. Files and Curves (10)

Files (7)

Curves (3)