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3abz

Crystal structure of Se-Met labeled Beta-glucosidase from Kluyveromyces marxianus

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Beta-glucosidase I

Kluyveromyces marxianus

UniProt D1GCC6

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein homooligomer Homooligomer Protein 4 GLYCEROL × 8 water × 4 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer
3abz 3ac0

2 assemblies

Other homooligomers

None

Heteromeric or nucleic-acid complex

None

View Construct and Data Evidence
UniProt name D1GCC6_KLUMA
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–845； UniProt 1–845 Author chain B； PDBConstruct 1–845； UniProt 1–845 Author chain C； PDBConstruct 1–845； UniProt 1–845 Author chain D； PDBConstruct 1–845； UniProt 1–845

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id3abz
Deposition date deposition_date2009-12-25
Structure title titleCrystal structure of Se-Met labeled Beta-glucosidase from Kluyveromyces marxianus
Keywords keywordsGlycoside hydrolase family3 beta-glucosidase, PA14 domain, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3abz__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3abz__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 109 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

3abz__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）48.65 Å
Rg (electron density)48.37 Å
Total Rg48.50 Å
Atom count26076
Residues3283
Excluded volume464410 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3abz__assembly_1__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

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6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

Domain ID domain_idd3abza1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.8 — (Trans)glycosidases
Family Family familyc.1.8.7 — NagZ-like
Domain ID domain_idd3abza2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.11 — Beta-D-glucan exohydrolase, C-terminal domain-like
Family Family familyc.23.11.1 — Beta-D-glucan exohydrolase, C-terminal domain-like
Domain ID domain_idd3abza3
Class classb — All beta proteins
Fold Fold foldb.179 — Anthrax protective antigen N-terminal-like
Superfamily Superfamily superfamilyb.179.1 — PA14-like
Family Family familyb.179.1.1 — PA14
Domain ID domain_idd3abza4
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.31 — Fibronectin III-like
Family Family familyb.1.31.1 — Fibronectin III-like
Domain ID domain_idd3abzb1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.8 — (Trans)glycosidases
Family Family familyc.1.8.7 — NagZ-like
Domain ID domain_idd3abzb2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.11 — Beta-D-glucan exohydrolase, C-terminal domain-like
Family Family familyc.23.11.1 — Beta-D-glucan exohydrolase, C-terminal domain-like
Domain ID domain_idd3abzb3
Class classb — All beta proteins
Fold Fold foldb.179 — Anthrax protective antigen N-terminal-like
Superfamily Superfamily superfamilyb.179.1 — PA14-like
Family Family familyb.179.1.1 — PA14
Domain ID domain_idd3abzb4
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.31 — Fibronectin III-like
Family Family familyb.1.31.1 — Fibronectin III-like
Domain ID domain_idd3abzc1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.8 — (Trans)glycosidases
Family Family familyc.1.8.7 — NagZ-like
Domain ID domain_idd3abzc2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.11 — Beta-D-glucan exohydrolase, C-terminal domain-like
Family Family familyc.23.11.1 — Beta-D-glucan exohydrolase, C-terminal domain-like
Domain ID domain_idd3abzc3
Class classb — All beta proteins
Fold Fold foldb.179 — Anthrax protective antigen N-terminal-like
Superfamily Superfamily superfamilyb.179.1 — PA14-like
Family Family familyb.179.1.1 — PA14
Domain ID domain_idd3abzc4
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.31 — Fibronectin III-like
Family Family familyb.1.31.1 — Fibronectin III-like
Domain ID domain_idd3abzd1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.8 — (Trans)glycosidases
Family Family familyc.1.8.7 — NagZ-like
Domain ID domain_idd3abzd2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.11 — Beta-D-glucan exohydrolase, C-terminal domain-like
Family Family familyc.23.11.1 — Beta-D-glucan exohydrolase, C-terminal domain-like
Domain ID domain_idd3abzd3
Class classb — All beta proteins
Fold Fold foldb.179 — Anthrax protective antigen N-terminal-like
Superfamily Superfamily superfamilyb.179.1 — PA14-like
Family Family familyb.179.1.1 — PA14
Domain ID domain_idd3abzd4
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.31 — Fibronectin III-like
Family Family familyb.1.31.1 — Fibronectin III-like

CATH v4.4 (16 domains)

Domain ID domain_id3abzA01
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily300 — Glycoside hydrolase, family 3, N-terminal domain
Domain ID domain_id3abzA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1700 — Glycoside hydrolase family 3 C-terminal domain
Domain ID domain_id3abzA03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily260 — Galactose-binding domain-like
Domain ID domain_id3abzA04
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3abzB01
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily300 — Glycoside hydrolase, family 3, N-terminal domain
Domain ID domain_id3abzB02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1700 — Glycoside hydrolase family 3 C-terminal domain
Domain ID domain_id3abzB03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily260 — Galactose-binding domain-like
Domain ID domain_id3abzB04
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3abzC01
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily300 — Glycoside hydrolase, family 3, N-terminal domain
Domain ID domain_id3abzC02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1700 — Glycoside hydrolase family 3 C-terminal domain
Domain ID domain_id3abzC03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily260 — Galactose-binding domain-like
Domain ID domain_id3abzC04
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3abzD01
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily300 — Glycoside hydrolase, family 3, N-terminal domain
Domain ID domain_id3abzD02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1700 — Glycoside hydrolase family 3 C-terminal domain
Domain ID domain_id3abzD03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily260 — Galactose-binding domain-like
Domain ID domain_id3abzD04
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
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7. Citations (2)