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1c7j

PNB ESTERASE 56C8

Method: X-RAY DIFFRACTION Dmax: 72.4 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN (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 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

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 1C7J 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
1QE3 PNB ESTERASE Deposited 1999-07-12 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）
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

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 1c7j

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1c7j
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1c7j
Deposition date deposition_date2000-02-21
Structure title titlePNB ESTERASE 56C8
Keywords keywordsALPHA-BETA HYDROLASE, DIRECTED EVOLUTION, ORGANIC ACTIVITY, PNB ESTERASE, 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_guinier23.35 Å
Radius of gyration Rg (electron density) rg_electron22.01 Å
Forward intensity I(0) i046343100.00
Molecular weight molecular_weight53583.0 kDa
Excluded volume excluded_volume67288 ų
Envelope volume envelope_volume78364 ų
Hydration-shell volume shell_volume28599 ų
Envelope diameter envelope_diameter74.5 Å
Shell Rg shell_rg29.93 Å
Envelope Rg envelope_rg22.30 Å
Shape Rg shape_rg21.99 Å
Total Rg total_rg23.01 Å
Total atoms total_atoms3785
Residues n_residues485
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 dmax72.4 Å
Rg (real space) rg_real23.20 Å
Rg uncertainty (real space) rg_real_error0.35 Å
I(0) (real space) i0_real4.6340e+07
I(0) uncertainty (real space) i0_real_error5.5080e+05
Rg (reciprocal space) rg_reciprocal23.24 Å
I(0) (reciprocal space) i0_reciprocal46340000.0000
Solution quality estimate total_estimate0.9004
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary71.3 Å
Skewness Skewness skewness0.148
Kurtosis Kurtosis kurtosis-0.441
Angular range angular_range— – 0.3400 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha15310000.0000
Real-space data points n_real_points66
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.907; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; 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_idd1c7ja_
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_id1c7jA00
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)