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1qe3

PNB ESTERASE

Method: X-RAY DIFFRACTION Dmax: 71.1 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PARA-NITROBENZYL ESTERASE

Bacillus subtilis

UniProt P37967

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 1–489 Not recorded SO4 SULFATE ION × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.25；291 K；28% PEG 4000, 150 LIS04,100MM TRIS, pH 8.25, VAPOR DIFFUSION, HANGING DROP, temperature 18K Resolution 1.50 Å R-free 0.240

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 1QE3 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1C7I THERMOPHYLIC PNB ESTERASE Deposited 2000-02-21 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–489（489 aa）
Mutation：A56V, I60V, T73K, L144M, L313F, H322Y, A343V, M358V, Y370F, A400T, G412E, I437T, T459S CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；20% PEG 4000, 100MM TRIS, 200MM MGAC, pH 7.50
Resolution 2.00 Å R-free 0.245
1C7J PNB ESTERASE 56C8 Deposited 2000-02-21 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–489（489 aa）
Mutation：I60V, L144M, P317S, H322R, L334S, M358V, Y370F, SO4 SULFATE ION × 1 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.4；29% PEG 4000, 100MM TRIS, 175 LISO4, 10MM DMF, pH 8.40
Resolution 1.60 Å R-free 0.228

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PNBA_BACSU
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–489； UniProt 1–489

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 1qe3

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1qe3
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1qe3
Deposition date deposition_date1999-07-12
Structure title titlePNB ESTERASE
Keywords keywordsALPHA-BETA HYDROLASE DIRECTED EVOLUTION, 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_guinier23.28 Å
Radius of gyration Rg (electron density) rg_electron21.92 Å
Forward intensity I(0) i043004800.00
Molecular weight molecular_weight51650.0 kDa
Excluded volume excluded_volume64871 ų
Envelope volume envelope_volume75046 ų
Hydration-shell volume shell_volume27585 ų
Envelope diameter envelope_diameter71.5 Å
Shell Rg shell_rg29.68 Å
Envelope Rg envelope_rg22.22 Å
Shape Rg shape_rg21.89 Å
Total Rg total_rg22.92 Å
Total atoms total_atoms3649
Residues n_residues467
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 dmax71.1 Å
Rg (real space) rg_real23.14 Å
Rg uncertainty (real space) rg_real_error0.35 Å
I(0) (real space) i0_real4.3000e+07
I(0) uncertainty (real space) i0_real_error4.6480e+05
Rg (reciprocal space) rg_reciprocal23.17 Å
I(0) (reciprocal space) i0_reciprocal43010000.0000
Solution quality estimate total_estimate0.9074
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.4 Å
Skewness Skewness skewness0.153
Kurtosis Kurtosis kurtosis-0.479
Angular range angular_range— – 0.3400 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha12190000.0000
Real-space data points n_real_points66
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.936; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.996
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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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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1qe3a_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamilyc.69.1 — alpha/beta-Hydrolases
Family Family familyc.69.1.1 — Acetylcholinesterase-like

CATH v4.4 (1 domains)

Domain ID domain_id1qe3A00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1820 — Alpha/Beta hydrolase fold, catalytic domain
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8. Citations (1)

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9. Files and Curves (10)