SAXSdb — 1bqg

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

D-GLUCARATE DEHYDRATASE

Pseudomonas putida

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–451	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；pH 7	Resolution 2.30 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	GUDH_PSEPU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–451； UniProt 1–451

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	1bqg
Deposition date deposition_date	1998-08-15
Structure title title	THE STRUCTURE OF THE D-GLUCARATE DEHYDRATASE PROTEIN FROM PSEUDOMONAS PUTIDA
Keywords keywords	GLUCARATE, TIM BARREL, ENOLASE SUPERFAMILY; GLUCARATE
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	21.97 Å
Radius of gyration Rg (electron density) rg_electron	20.84 Å
Forward intensity I(0) i0	32264600.00
Molecular weight molecular_weight	43007.0 kDa
Excluded volume excluded_volume	53483 Å³
Envelope volume envelope_volume	61365 Å³
Hydration-shell volume shell_volume	24068 Å³
Envelope diameter envelope_diameter	71.4 Å
Shell Rg shell_rg	27.84 Å
Envelope Rg envelope_rg	21.02 Å
Shape Rg shape_rg	20.83 Å
Total Rg total_rg	21.72 Å
Total atoms total_atoms	3033
Residues n_residues	399
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	68.7 Å
Rg (real space) rg_real	21.83 Å
Rg uncertainty (real space) rg_real_error	0.32 Å
I(0) (real space) i0_real	3.2260e+07
I(0) uncertainty (real space) i0_real_error	3.7920e+05
Rg (reciprocal space) rg_reciprocal	21.86 Å
I(0) (reciprocal space) i0_reciprocal	32270000.0000
Solution quality estimate total_estimate	0.9019
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.6 Å
Skewness Skewness skewness	0.177
Kurtosis Kurtosis kurtosis	-0.473
Angular range angular_range	— – 0.3600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9164000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.917; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.971

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	D-GLUCARATE DEHYDRATASE
Molecular weight formula_weight	49632.0 kDa
EC 编号 ec_number	4.2.1.40
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3178

MEALNQSQAATGAPVITDLKVVPVAGHDSMLLNLSGAHGPLFTRNILILTDSSGHVGVGEVPGGEGIRKTLEDARHLLINQSIGNYQSLLNKVRNAFADRDVGGRGLQTFDLRIAVHAVTAVESALLDLLGQHLQVPVAALLGEGQQRDAVEMLGYLFYVGDRNKTDLGYRSEHEADNEWFRLRNKEALTPESVVALAEAAYDRYGFKDFKLKGGVLRGEDEIAAVTALSERFPDARITLDPNGAWSLKEAVALCRDQHHVLAYAEDPCGAENGYSGREVMAEFRRSTGLRTATNMIATDWRQMGHAIQLQSVDIPLADPHFWTMQGSVRVAQMCNEWGLTWGSHSNNHFDISLAMFTHVAAAAPGNITAIDTHWIWQDGQRLTKEPLQIKGGLVEVPKKPGLGVELDWDALMKAHEVYKSMGLGARDDATAMRYLVSGWEFNNKRPCMVR

来源 Source

来源生物 organism	Pseudomonas putida
NCBI Class编号 ncbi_taxonomy_id	303
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	145

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1bqga1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.11 — Enolase C-terminal domain-like
Family Family family	c.1.11.2 — D-glucarate dehydratase-like

Domain ID domain_id	d1bqga2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.54 — Enolase N-terminal domain-like
Superfamily Superfamily superfamily	d.54.1 — Enolase N-terminal domain-like
Family Family family	d.54.1.1 — Enolase N-terminal domain-like

CATH v4.4 (2 domains)

Domain ID domain_id	1bqgA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	10 — Enolase-like, N-terminal domain

Domain ID domain_id	1bqgA02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	120 — Enolase-like C-terminal domain

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8. Citations (1)

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Unit-cell length a length_a	69.623 Å
Unit-cell length b length_b	108.786 Å
Unit-cell length c length_c	122.573 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	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	—
R_work r_work	0.1900
R_free r_free	—

fit	/app/data/saxs_computation/bq/1bqg/1bqg.fit
pddf	/app/data/pr_computation/bq/1bqg/1bqg.pr.out
profile	/app/data/saxs_computation/bq/1bqg/1bqg.dat

THE STRUCTURE OF THE D-GLUCARATE DEHYDRATASE PROTEIN FROM PSEUDOMONAS PUTIDA

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

D-GLUCARATE DEHYDRATASE

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