1bg6

CRYSTAL STRUCTURE OF THE N-(1-D-CARBOXYLETHYL)-L-NORVALINE DEHYDROGENASE FROM ARTHROBACTER SP. STRAIN 1C

Method: X-RAY DIFFRACTION D_max: 62.4 Å Quality: EXCELLENT

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

N-(1-D-CARBOXYLETHYL)-L-NORVALINE DEHYDROGENASE

Arthrobacter sp.

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 1–359	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6；pH 6.0	Resolution 1.80 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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	ODH_ARTSC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–359； UniProt 1–359

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	1bg6
Deposition date deposition_date	1998-06-05
Structure title title	CRYSTAL STRUCTURE OF THE N-(1-D-CARBOXYLETHYL)-L-NORVALINE DEHYDROGENASE FROM ARTHROBACTER SP. STRAIN 1C
Keywords keywords	(D, L) STEREOSPECIFIC OPINE 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	20.95 Å
Radius of gyration Rg (electron density) rg_electron	19.75 Å
Forward intensity I(0) i0	22134000.00
Molecular weight molecular_weight	36773.0 kDa
Excluded volume excluded_volume	46431 Å³
Envelope volume envelope_volume	53550 Å³
Hydration-shell volume shell_volume	22269 Å³
Envelope diameter envelope_diameter	62.7 Å
Shell Rg shell_rg	26.52 Å
Envelope Rg envelope_rg	19.72 Å
Shape Rg shape_rg	19.74 Å
Total Rg total_rg	20.67 Å
Total atoms total_atoms	2592
Residues n_residues	349
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	62.4 Å
Rg (real space) rg_real	20.79 Å
Rg uncertainty (real space) rg_real_error	0.32 Å
I(0) (real space) i0_real	2.2130e+07
I(0) uncertainty (real space) i0_real_error	2.8060e+05
Rg (reciprocal space) rg_reciprocal	20.82 Å
I(0) (reciprocal space) i0_reciprocal	22130000.0000
Solution quality estimate total_estimate	0.9093
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.2 Å
Skewness Skewness skewness	0.068
Kurtosis Kurtosis kurtosis	-0.587
Angular range angular_range	— – 0.3800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4397000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.953; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.973

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1bg6a1
Class class	a — All alpha proteins
Fold Fold fold	a.100 — 6-phosphogluconate dehydrogenase C-terminal domain-like
Superfamily Superfamily superfamily	a.100.1 — 6-phosphogluconate dehydrogenase C-terminal domain-like
Family Family family	a.100.1.5 — N-(1-D-carboxylethyl)-L-norvaline dehydrogenase

Domain ID domain_id	d1bg6a2
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.2.1.6 — 6-phosphogluconate dehydrogenase-like, N-terminal domain

CATH v4.4 (2 domains)

Domain ID domain_id	1bg6A01
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	1bg6A02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1040 — N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2
Homologous superfamily homologous superfamily	10 — N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2

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8. Citations (2)

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Unit-cell length a length_a	104.900 Å
Unit-cell length b length_b	80.000 Å
Unit-cell length c length_c	45.500 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	4

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Description description	N-(1-D-CARBOXYLETHYL)-L-NORVALINE DEHYDROGENASE
Molecular weight formula_weight	37969.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2705

CRYSTAL STRUCTURE OF THE N-(1-D-CARBOXYLETHYL)-L-NORVALINE DEHYDROGENASE FROM ARTHROBACTER SP. STRAIN 1C

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

N-(1-D-CARBOXYLETHYL)-L-NORVALINE 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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Arthrobacter sp.
NCBI Class编号 ncbi_taxonomy_id	79670
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	113

fit	/app/data/saxs_computation/bg/1bg6/1bg6.fit
pddf	/app/data/pr_computation/bg/1bg6/1bg6.pr.out
profile	/app/data/saxs_computation/bg/1bg6/1bg6.dat