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1kwf

Atomic Resolution Structure of an Inverting Glycosidase in Complex with Substrate

Method: X-RAY DIFFRACTION Dmax: 58.5 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Endoglucanase A

Clostridium thermocellum

UniProt P04955

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 33–395 Fragment：catalytic core (residues 33-395) Mutation：E95Q beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose × 1 BGC beta-D-glucopyranose × 3 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP Resolution 0.94 Å R-free 0.113

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 1KWF Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1CEM ENDOGLUCANASE A (CELA) CATALYTIC CORE, RESIDUES 33-395 Deposited 1995-12-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 33–395（363 aa） Fragment：CATALYTIC CORE RESIDUES 33-395
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.65 Å R-free 0.191
1IS9 Endoglucanase A from Clostridium thermocellum at atomic resolution Deposited 2001-11-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 33–395（363 aa） Fragment：residues 1-363
Not recorded HG MERCURY (II) ION × 6 CL CHLORIDE ION × 7 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.03 Å R-free 0.149

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

View Construct and Data Evidence
UniProt name GUNA_CLOTM
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–363； UniProt 33–395

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 1kwf

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1kwf
Deposition date deposition_date2002-01-29
Structure title titleAtomic Resolution Structure of an Inverting Glycosidase in Complex with Substrate
Keywords keywordshydrolase, inverting glycosidase, atomic resolution, protein-carbohydrate interactions, reaction mechanism, cellulase; 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_guinier19.96 Å
Radius of gyration Rg (electron density) rg_electron18.59 Å
Forward intensity I(0) i029460800.00
Molecular weight molecular_weight41058.0 kDa
Excluded volume excluded_volume50802 ų
Envelope volume envelope_volume54342 ų
Hydration-shell volume shell_volume23231 ų
Envelope diameter envelope_diameter58.2 Å
Shell Rg shell_rg26.16 Å
Envelope Rg envelope_rg18.83 Å
Shape Rg shape_rg18.57 Å
Total Rg total_rg19.52 Å
Total atoms total_atoms2901
Residues n_residues363
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 dmax58.5 Å
Rg (real space) rg_real19.75 Å
Rg uncertainty (real space) rg_real_error0.25 Å
I(0) (real space) i0_real2.9460e+07
I(0) uncertainty (real space) i0_real_error3.3360e+05
Rg (reciprocal space) rg_reciprocal19.78 Å
I(0) (reciprocal space) i0_reciprocal29460000.0000
Solution quality estimate total_estimate0.9066
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.3 Å
Skewness Skewness skewness0.003
Kurtosis Kurtosis kurtosis-0.556
Angular range angular_range— – 0.4000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9714000.0000
Real-space data points n_real_points72
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.937; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; Smooth: 0.999
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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_idd1kwfa_
Class classa — All alpha proteins
Fold Fold folda.102 — alpha/alpha toroid
Superfamily Superfamily superfamilya.102.1 — Six-hairpin glycosidases
Family Family familya.102.1.2 — Cellulases catalytic domain

CATH v4.4 (1 domains)

Domain ID domain_id1kwfA00
Class class1 — Mainly Alpha
Architecture architecture50 — Alpha/alpha barrel
Topology topology10 — Glycosyltransferase
Homologous superfamily homologous superfamily10 —
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8. Citations (3)

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9. Files and Curves (10)