SAXSdb — 1bxk

▼

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

PROTEIN (DTDP-GLUCOSE 4,6-DEHYDRATASE)

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 1–350 Chain B； UniProt 1–350	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6；15% PEG 8000 100 MM K/MES PH 6.0	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.

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

View Construct and Data Evidence

UniProt name	RFFG_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–355； UniProt 1–350 Author chain B； PDBConstruct 1–355； UniProt 1–350

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1bxk
Deposition date deposition_date	1998-10-05
Structure title title	DTDP-GLUCOSE 4,6-DEHYDRATASE FROM E. COLI
Keywords keywords	EPIMERASE, DEHYDRATASE, DEHYDROGENASE, LYASE; LYASE
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	29.01 Å
Radius of gyration Rg (electron density) rg_electron	28.43 Å
Forward intensity I(0) i0	99940200.00
Molecular weight molecular_weight	77820.0 kDa
Excluded volume excluded_volume	96788 Å³
Envelope volume envelope_volume	116660 Å³
Hydration-shell volume shell_volume	34682 Å³
Envelope diameter envelope_diameter	109.1 Å
Shell Rg shell_rg	35.28 Å
Envelope Rg envelope_rg	28.59 Å
Shape Rg shape_rg	28.41 Å
Total Rg total_rg	29.09 Å
Total atoms total_atoms	5487
Residues n_residues	685
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

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	103.6 Å
Rg (real space) rg_real	29.07 Å
Rg uncertainty (real space) rg_real_error	0.94 Å
I(0) (real space) i0_real	9.9940e+07
I(0) uncertainty (real space) i0_real_error	1.5780e+06
Rg (reciprocal space) rg_reciprocal	29.04 Å
I(0) (reciprocal space) i0_reciprocal	99940000.0000
Solution quality estimate total_estimate	0.8426
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.1 Å
Skewness Skewness skewness	0.458
Kurtosis Kurtosis kurtosis	-0.135
Angular range angular_range	— – 0.2750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	29200000.0000
Real-space data points n_real_points	56
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.720; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.863; Smooth: 0.926

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	PROTEIN (DTDP-GLUCOSE 4,6-DEHYDRATASE)
Molecular weight formula_weight	39703.7 kDa
EC 编号 ec_number	4.2.1.46
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	5856

MRKILITGGAGFIGSALVRYIINETSDAVVVVDKLTYAGNLMSLAPVAQSERFAFEKVDICDRAELARVFTEHQPDCVMHLAAESHVDRSIDGPAAFIETNIVGTYTLLEAARAYWNALTEDKKSAFRFHHISTDEVYGDLHSTDDFFTETTPYAPSSPYSASKASSDHLVRAWLRTYGLPTLITNCSNNYGPYHFPEKLIPLMILNALAGKSLPVYGNGQQIRDWLYVEDHARALYCVATTGKVGETYNIGGHNERKNLDVVETICELLEELAPNKPHGVAHYRDLITFVADRPGHDLRYAIDASKIARELGCVPQETFESGMRKTVQWYLANESWWKQVQDGSYQGERLGLKG

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	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Molecular weight formula_weight	663.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	359

▼

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1bxka_
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.2.1.2 — Tyrosine-dependent oxidoreductases

Domain ID domain_id	d1bxkb_
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.2.1.2 — Tyrosine-dependent oxidoreductases

CATH v4.4 (4 domains)

Domain ID domain_id	1bxkA01
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	1bxkA02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	25 — UDP-galactose 4-epimerase; domain 1
Homologous superfamily homologous superfamily	10 — UDP-galactose 4-epimerase, domain 1

Domain ID domain_id	1bxkB01
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	1bxkB02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	25 — UDP-galactose 4-epimerase; domain 1
Homologous superfamily homologous superfamily	10 — UDP-galactose 4-epimerase, domain 1

▶

8. Citations (1)

▶

Unit-cell length a length_a	68.400 Å
Unit-cell length b length_b	109.200 Å
Unit-cell length c length_c	128.700 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	1.900 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	—
R_work r_work	0.1950
R_free r_free	—

fit	/app/data/saxs_computation/bx/1bxk/1bxk.fit
pddf	/app/data/pr_computation/bx/1bxk/1bxk.pr.out
profile	/app/data/saxs_computation/bx/1bxk/1bxk.dat

DTDP-GLUCOSE 4,6-DEHYDRATASE FROM E. COLI

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

PROTEIN (DTDP-GLUCOSE 4,6-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