SAXSdb — 1bkh

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

No usable UniProt protein identity is available for this entry.

七张关系表仍保留该条目的 assembly 与组成信息，但缺少统一蛋白身份时，不能可靠建立跨 PDB 的同蛋白Chain接。

Assembly Composition of the Current Entry

Assembly	Oligomeric State	实体与Construct证据	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer 蛋白 8 / DNA 0 / RNA 0 / 其他Polymer 0 PDB declaration: octameric	Entity 1：MUCONATE LACTONIZING ENZYME × 8 缺少 UniProt 身份时不显示参考序列区间	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.2；MUCONATE LACTONIZING ENZYME (MLE; 5-10 MG/ML) WAS DIALYZED AGAINST 0.2 MM MNCL2, 7 MM MERCAPTOETHANOL, 50 MM TRIS (PH 7), AND CIS, CIS-MUCONATE WAS ADDED TO A FINAL CONCENTRATION OF 0.2 MM. CRYSTALS WERE GROWN AT ROOM TEMPERATURE BY SITTING-DROP VAPOR DIFFUSION AGAINST A WELL SOLUTION OF 70 MM NACL, 70 MM SODIUM ACETATE (PH 5.2), 0.25% POLYETHYLENE GLYCOL (AVERAGE MOLECULAR WEIGHT 3350). DROPS CONTAINED EQUAL VOLUMES (10 MICRO L) OF WELL SOLUTION AND MLE., vapor diffusion - sitting drop	Resolution 2.10 Å
2	Protein homooligomer Homooligomer 蛋白 8 / DNA 0 / RNA 0 / 其他Polymer 0 PDB declaration: octameric	Entity 1：MUCONATE LACTONIZING ENZYME × 8 缺少 UniProt 身份时不显示参考序列区间	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.2；MUCONATE LACTONIZING ENZYME (MLE; 5-10 MG/ML) WAS DIALYZED AGAINST 0.2 MM MNCL2, 7 MM MERCAPTOETHANOL, 50 MM TRIS (PH 7), AND CIS, CIS-MUCONATE WAS ADDED TO A FINAL CONCENTRATION OF 0.2 MM. CRYSTALS WERE GROWN AT ROOM TEMPERATURE BY SITTING-DROP VAPOR DIFFUSION AGAINST A WELL SOLUTION OF 70 MM NACL, 70 MM SODIUM ACETATE (PH 5.2), 0.25% POLYETHYLENE GLYCOL (AVERAGE MOLECULAR WEIGHT 3350). DROPS CONTAINED EQUAL VOLUMES (10 MICRO L) OF WELL SOLUTION AND MLE., vapor diffusion - sitting drop	Resolution 2.10 Å

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	1bkh
Deposition date deposition_date	1998-07-07
Structure title title	MUCONATE LACTONIZING ENZYME FROM PSEUDOMONAS PUTIDA
Keywords keywords	MUCONATE LACTONIZING ENZYME, MUCONATE CYCLOISOMERASE AROMATIC HYDROCARBONS CATABOLISM, ISOMERASE, MUCONATE CYCLOISOMERASE; MUCONATE CYCLOISOMERASE
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	41.17 Å
Radius of gyration Rg (electron density) rg_electron	41.43 Å
Forward intensity I(0) i0	202269000.00
Molecular weight molecular_weight	115850.0 kDa
Excluded volume excluded_volume	145350 Å³
Envelope volume envelope_volume	188080 Å³
Hydration-shell volume shell_volume	40354 Å³
Envelope diameter envelope_diameter	144.6 Å
Shell Rg shell_rg	42.95 Å
Envelope Rg envelope_rg	41.08 Å
Shape Rg shape_rg	41.41 Å
Total Rg total_rg	41.56 Å
Total atoms total_atoms	8157
Residues n_residues	1078
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	137.2 Å
Rg (real space) rg_real	41.53 Å
Rg uncertainty (real space) rg_real_error	1.09 Å
I(0) (real space) i0_real	2.0230e+08
I(0) uncertainty (real space) i0_real_error	3.3230e+06
Rg (reciprocal space) rg_reciprocal	41.17 Å
I(0) (reciprocal space) i0_reciprocal	202200000.0000
Solution quality estimate total_estimate	0.8013
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	32.5 Å
Skewness Skewness skewness	0.498
Kurtosis Kurtosis kurtosis	-0.514
Angular range angular_range	— – 0.1900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	29270000.0000
Real-space data points n_real_points	39
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.735; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.755; Smooth: 0.453

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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) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1bkha1
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	d1bkha2
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

Domain ID domain_id	d1bkhb1
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	d1bkhb2
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

Domain ID domain_id	d1bkhc1
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	d1bkhc2
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 (6 domains)

Domain ID domain_id	1bkhA01
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	1bkhA02
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

Domain ID domain_id	1bkhB01
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	1bkhB02
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

Domain ID domain_id	1bkhC01
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	1bkhC02
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	136.180 Å
Unit-cell length b length_b	136.180 Å
Unit-cell length c length_c	265.110 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	48

Space group space_group	I 4 2 2
Space-group number int_tables_number	97
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	5.000 Å
R factor r_factor	0.1570
R_work r_work	0.1570
R_free r_free	—

Description description	MUCONATE LACTONIZING ENZYME
Molecular weight formula_weight	39878.6 kDa
EC 编号 ec_number	5.5.1.1
Source method src_method	man
Copy count entity_count	3

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	8721

MUCONATE LACTONIZING ENZYME FROM PSEUDOMONAS PUTIDA

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

Assembly Composition of the Current Entry

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) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Pseudomonas putida
NCBI Class编号 ncbi_taxonomy_id	303
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	564

fit	/app/data/saxs_computation/bk/1bkh/1bkh.fit
pddf	/app/data/pr_computation/bk/1bkh/1bkh.pr.out
profile	/app/data/saxs_computation/bk/1bkh/1bkh.dat