SAXSdb — 9yys

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

L-aminopeptidase/D-esterase

Jatrophihabitans endophyticus

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 1–285 Chain B； UniProt 1–285 Chain C； UniProt 1–285 Chain D； UniProt 1–285 Chain E； UniProt 1–285 Chain F； UniProt 1–285	Not recorded	PYRUVIC ACID × 3 GLYCEROL × 3 D-MALATE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.30 Å R-free 0.170

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	A0A1M5P6R3_9ACTN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–285； UniProt 1–285 Author chain B； PDBConstruct 1–285； UniProt 1–285 Author chain C； PDBConstruct 1–285； UniProt 1–285 Author chain D； PDBConstruct 1–285； UniProt 1–285 Author chain E； PDBConstruct 1–285； UniProt 1–285 Author chain F； PDBConstruct 1–285； UniProt 1–285

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	9yys
Deposition date deposition_date	2025-10-29
Structure title title	Crystal Structure of the Poly(Hexamethylene Adipamide) (Nylon66) Hydrolase Nyl10 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	36.62 Å
Radius of gyration Rg (electron density) rg_electron	35.88 Å
Forward intensity I(0) i0	446311000.00
Molecular weight molecular_weight	164900.0 kDa
Excluded volume excluded_volume	203890 Å³
Envelope volume envelope_volume	248830 Å³
Hydration-shell volume shell_volume	56465 Å³
Envelope diameter envelope_diameter	119.2 Å
Shell Rg shell_rg	43.35 Å
Envelope Rg envelope_rg	35.55 Å
Shape Rg shape_rg	35.90 Å
Total Rg total_rg	36.25 Å
Total atoms total_atoms	11603
Residues n_residues	1639
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	119.0 Å
Rg (real space) rg_real	36.54 Å
Rg uncertainty (real space) rg_real_error	0.78 Å
I(0) (real space) i0_real	4.4630e+08
I(0) uncertainty (real space) i0_real_error	7.4950e+06
Rg (reciprocal space) rg_reciprocal	36.59 Å
I(0) (reciprocal space) i0_reciprocal	446300000.0000
Solution quality estimate total_estimate	0.8970
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	44.3 Å
Skewness Skewness skewness	0.256
Kurtosis Kurtosis kurtosis	-0.494
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	135200000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.908; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.936

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	L-aminopeptidase/D-esterase
Molecular weight formula_weight	28916.5 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	12497

MTAFGVDGVRVGHWSDPDAATGCTVVELPPGTVASYEVRGGAPASRELIALEPDKSVTAVDAVLLTGGSAFGLAAADGVMRRLEEAGRGVTTPAGVVPIVAAMALYDLAAGDASVRPGPAEGYAAARDVGTDVALHGRIGAGTGAHVGNWRGVDGRRPGGLGHAVRRLDDVVVAALCAVNAFGDIDDGHDEVVLDALRALPRPFDFERTNTTIGVVVTNARLDKTACRTVAQGAHDGLARAITPPHTRVDGDGFVAAATGEVEAHVDVVRLLALAAVTAAIRSVA

来源 Source

来源生物 organism	Jatrophihabitans endophyticus
NCBI Class编号 ncbi_taxonomy_id	1206085
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	PYRUVIC ACID
Molecular weight formula_weight	88.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	D-MALATE
Molecular weight formula_weight	134.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	775

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8. Citations (1)

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Unit-cell length a length_a	83.126 Å
Unit-cell length b length_b	120.193 Å
Unit-cell length c length_c	148.305 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.99 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.300 Å
Low-resolution limit resolution_low	68.400 Å
R factor r_factor	0.1439
R_work r_work	0.1425
R_free r_free	0.1701

fit	/app/data/saxs_computation/yy/9yys/9yys.fit
pddf	/app/data/pr_computation/yy/9yys/9yys.pr.out
profile	/app/data/saxs_computation/yy/9yys/9yys.dat

Crystal Structure of the Poly(Hexamethylene Adipamide) (Nylon66) Hydrolase Nyl10 at Cryo Temperature

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

L-aminopeptidase/D-esterase

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