2vjd

Torpedo Californica Acetylcholinesterase In Complex With A Non Hydrolysable Substrate Analogue, 4-Oxo-N,N,N- Trimethylpentanaminium - Orthorhombic space group - Dataset C at 150K

Method: X-RAY DIFFRACTION Dmax: 130.2 Å Quality: GOOD

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

ACETYLCHOLINESTERASE

OrganismNot specified

UniProt P04058

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 22–558 Chain B; UniProt 22–558 Fragment:RESIDUES 22-558 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CL CHLORIDE ION × 4 CCD (4R)-4-HYDROXY-N,N,N-TRIMETHYLPENTAN-1-AMINIUM × 4 PGE TRIETHYLENE GLYCOL × 3 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6;277 K;32% PEG200, 150MM MES, PH6, 4 DEG. C. 2 HOURS SOAKING IN MOTHER LIQUOR SOLUTION CONTAINING 0.5 MM OTMA, pH 6.0 Resolution 2.30 Å R-free 0.250

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.

124 other PDB entries and 125 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ACES_TORCA
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–537; UniProt 22–558 Author chain B; PDBConstruct 1–537; UniProt 22–558

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 2vjd

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2vjd
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2vjd
Deposition date deposition_date2007-12-09
Structure title titleTorpedo Californica Acetylcholinesterase In Complex With A Non Hydrolysable Substrate Analogue, 4-Oxo-N,N,N- Trimethylpentanaminium - Orthorhombic space group - Dataset C at 150K
Keywords keywords;SERINE ESTERASE, ALTERNATIVE SPLICING, NEUROTRANSMITTER DEGRADATION, KINETIC CRYSTALLOGRAPHY, STRUCTURAL DYNAMICS, XRAY DAMAGE, SUBSTRATE ANALOGUE, LIPOPROTEIN, GLYCOPROTEIN, CELL JUNCTION, SYNAPSE, MEMBRANE, HYDROLASE, GPI-ANCHOR ;; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier38.42
Radius of gyration Rg (electron density) rg_electron38.47
Forward intensity I(0) i0218020000.00
Molecular weight molecular_weight121730.0 kDa
Excluded volume excluded_volume152760 ų
Envelope volume envelope_volume187850 ų
Hydration-shell volume shell_volume42430 ų
Envelope diameter envelope_diameter137.0
Shell Rg shell_rg42.16
Envelope Rg envelope_rg38.26
Shape Rg shape_rg38.43
Total Rg total_rg38.80
Total atoms total_atoms8584
Residues n_residues1060
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax130.2
Rg (real space) rg_real38.81
Rg uncertainty (real space) rg_real_error1.17
I(0) (real space) i0_real2.1800e+08
I(0) uncertainty (real space) i0_real_error3.8630e+06
Rg (reciprocal space) rg_reciprocal38.58
I(0) (reciprocal space) i0_reciprocal218000000.0000
Solution quality estimate total_estimate0.7960
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary34.9
Skewness Skewness skewness0.474
Kurtosis Kurtosis kurtosis-0.597
Angular range angular_range— – 0.2050 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha62460000.0000
Real-space data points n_real_points42
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.608; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.786; Smooth: 0.735

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2vjda_
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
Domain ID domain_idd2vjdb_
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 (2 domains)

Domain ID domain_id2vjdA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1820 — Alpha/Beta hydrolase fold, catalytic domain
Domain ID domain_id2vjdB00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1820 — Alpha/Beta hydrolase fold, catalytic domain

8. Citations (1)

9. Files and Curves (10)