SAXSdb — 9z0b

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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 4 / DNA 0 / RNA 0 / 其他Polymer 0 PDB declaration: tetrameric	Entity 1：Poly (caprolactam and hexamethylene adipamide) hydrolase Nyl12 × 4 缺少 UniProt 身份时不显示参考序列区间	Not recorded	CHOLINE ION × 2 ACETATE ION × 2 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.75 Å R-free 0.197
2	Protein homooligomer Homooligomer 蛋白 4 / DNA 0 / RNA 0 / 其他Polymer 0 PDB declaration: tetrameric	Entity 1：Poly (caprolactam and hexamethylene adipamide) hydrolase Nyl12 × 4 缺少 UniProt 身份时不显示参考序列区间	Not recorded	CHOLINE ION × 1 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 GLYCEROL × 2 1,2-ETHANEDIOL × 1 DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.75 Å R-free 0.197

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	9z0b
Deposition date deposition_date	2025-10-31
最后修订 last_revision	2026-06-03
Structure title title	Crystal Structure of the Polycaprolactam (Nylon6) and Poly(Hexamethylene Adipamide) (Nylon66) Hydrolase Nyl12 at Cryo Temperature
Keywords keywords	Nylon hydrolase, amidase, Ntn-hydrolase, amide bond hydrolase, HYDROLASE; HYDROLASE
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	44.31 Å
Radius of gyration Rg (electron density) rg_electron	43.68 Å
Forward intensity I(0) i0	960643000.00
Molecular weight molecular_weight	266900.0 kDa
Excluded volume excluded_volume	338370 Å³
Envelope volume envelope_volume	440270 Å³
Hydration-shell volume shell_volume	80864 Å³
Envelope diameter envelope_diameter	142.3 Å
Shell Rg shell_rg	50.99 Å
Envelope Rg envelope_rg	43.13 Å
Shape Rg shape_rg	43.67 Å
Total Rg total_rg	44.03 Å
Total atoms total_atoms	18862
Residues n_residues	2484
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	136.8 Å
Rg (real space) rg_real	44.02 Å
Rg uncertainty (real space) rg_real_error	1.16 Å
I(0) (real space) i0_real	9.6060e+08
I(0) uncertainty (real space) i0_real_error	1.7320e+07
Rg (reciprocal space) rg_reciprocal	44.31 Å
I(0) (reciprocal space) i0_reciprocal	961000000.0000
Solution quality estimate total_estimate	0.8974
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	60.8 Å
Skewness Skewness skewness	0.020
Kurtosis Kurtosis kurtosis	-0.585
Angular range angular_range	— – 0.1800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	129500000.0000
Real-space data points n_real_points	37
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.923; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.917

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	Poly (caprolactam and hexamethylene adipamide) hydrolase Nyl12
Molecular weight formula_weight	35143.9 kDa
EC 编号 ec_number	3.5.1.117
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	19711

MAASSTDNILHFDFPEVQIGTAINPEGPTGITLFYFPKGVQASVDIQGGSVGTFFTQEKMQQGEAYLDGVAFTGGGILGLEAVAGAVSSLFADQTKNEVQFRRMPLISGAVIFDYTPRQNMIYPDKALGQKAFAALSAGQFVQGRHGAGVSASVGKLLRDGFQLAGQGGAFAQIGKTKIAVFTVVNAVGVILDEKGEVIYGLPKGATKQTLNQQVTELLQQPKKPFWPEPKNTTLTIVITNEKLAPRHLKQLGRQVHHALSQVIHPYATILDGDVLYTVSTRSIESDLYAPGADIESDLNAKFIYLGMVAGELAKQAVWSAVGYSHRP

来源 Source

来源生物 organism	Gammaproteobacteria bacterium
NCBI Class编号 ncbi_taxonomy_id	1913989
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	CHOLINE ION
Molecular weight formula_weight	104.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	831

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8. Citations (1)

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Unit-cell length a length_a	119.623 Å
Unit-cell length b length_b	135.407 Å
Unit-cell length c length_c	142.882 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	32

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.750 Å
Low-resolution limit resolution_low	98.280 Å
R factor r_factor	0.1629
R_work r_work	0.1612
R_free r_free	0.1965

fit	/app/data/saxs_computation/z0/9z0b/9z0b.fit
pddf	/app/data/pr_computation/z0/9z0b/9z0b.pr.out
profile	/app/data/saxs_computation/z0/9z0b/9z0b.dat

Crystal Structure of the Polycaprolactam (Nylon6) and Poly(Hexamethylene Adipamide) (Nylon66) Hydrolase Nyl12 at Cryo Temperature

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