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9xv8

Catalytic domain of N1484 E121S variant

Method: X-RAY DIFFRACTION Dmax: 87.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Lipase

Micromonospora ureilytica

UniProt A0A3N9XER1

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 54–312 Not recorded SULFATE ION × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 1.64 Å R-free 0.225
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 54–312 Not recorded SULFATE ION × 1 GLYCEROL × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 1.64 Å R-free 0.225

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.

Other PDB Difference from Current Entry 9XV8 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9XV5 Catalytic domain of N1484 Deposited 2025-11-25 Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 54–312（259 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.40 Å R-free 0.177

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A3N9XER1_9ACTN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–260； UniProt 54–312 Author chain B； PDBConstruct 2–260； UniProt 54–312

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.

SAXS scattering curve SAXS Profile

SAXS profile for 9xv8

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9xv8
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9xv8
Deposition date deposition_date2025-11-26
最后修订 last_revision2026-06-03
Structure title titleCatalytic domain of N1484 E121S variant
Keywords keywordsPET hydrolase, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier27.42 Å
Radius of gyration Rg (electron density) rg_electron26.89 Å
Forward intensity I(0) i051139700.00
Molecular weight molecular_weight54767.0 kDa
Excluded volume excluded_volume68065 ų
Envelope volume envelope_volume78096 ų
Hydration-shell volume shell_volume25186 ų
Envelope diameter envelope_diameter90.3 Å
Shell Rg shell_rg32.90 Å
Envelope Rg envelope_rg26.98 Å
Shape Rg shape_rg26.89 Å
Total Rg total_rg27.50 Å
Total atoms total_atoms3851
Residues n_residues513
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax87.2 Å
Rg (real space) rg_real27.63 Å
Rg uncertainty (real space) rg_real_error0.57 Å
I(0) (real space) i0_real5.1140e+07
I(0) uncertainty (real space) i0_real_error6.5240e+05
Rg (reciprocal space) rg_reciprocal27.57 Å
I(0) (reciprocal space) i0_reciprocal51140000.0000
Solution quality estimate total_estimate0.8520
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.5 Å
Skewness Skewness skewness0.473
Kurtosis Kurtosis kurtosis-0.533
Angular range angular_range— – 0.2900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha13870000.0000
Real-space data points n_real_points59
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.794; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.906; Smooth: 0.784
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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8. Citations (1)

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9. Files and Curves (10)