6x1q

1.8 Angstrom resolution structure of b-galactosidase with a 200 kV cryoARM electron microscope

Method: ELECTRON MICROSCOPY Dmax: 174.2 Å Quality: GOOD

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

Beta-galactosidase

OrganismNot specified

UniProt P00722

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 3–1023 Chain B; UniProt 3–1023 Chain C; UniProt 3–1023 Chain D; UniProt 3–1023 Not recorded MG MAGNESIUM ION × 8 NA SODIUM ION × 8 ELECTRON MICROSCOPY cryo-EM buffer:pH 8;25mM Tris pH 8.0, 50mM NaCl, 0.5mM TCEP, 2mM MgCl cryo-EM vitrification conditions:Cryogen ETHANE Resolution 1.80 Å

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.

67 other PDB entries and 83 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BGAL_ECOLI
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–1021; UniProt 3–1023 Author chain B; PDBConstruct 1–1021; UniProt 3–1023 Author chain C; PDBConstruct 1–1021; UniProt 3–1023 Author chain D; PDBConstruct 1–1021; UniProt 3–1023

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 6x1q

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6x1q
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6x1q
Deposition date deposition_date2020-05-19
Structure title title1.8 Angstrom resolution structure of b-galactosidase with a 200 kV cryoARM electron microscope
Keywords keywordsenzyme, HYDROLASE; HYDROLASE
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier51.40
Radius of gyration Rg (electron density) rg_electron51.06
Forward intensity I(0) i03009250000.00
Molecular weight molecular_weight452850.0 kDa
Excluded volume excluded_volume562200 ų
Envelope volume envelope_volume715620 ų
Hydration-shell volume shell_volume112200 ų
Envelope diameter envelope_diameter181.2
Shell Rg shell_rg58.47
Envelope Rg envelope_rg50.17
Shape Rg shape_rg51.05
Total Rg total_rg51.29
Total atoms total_atoms62520
Residues n_residues4056
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 dmax174.2
Rg (real space) rg_real51.29
Rg uncertainty (real space) rg_real_error1.28
I(0) (real space) i0_real3.0090e+09
I(0) uncertainty (real space) i0_real_error6.1640e+07
Rg (reciprocal space) rg_reciprocal51.47
I(0) (reciprocal space) i0_reciprocal3010000000.0000
Solution quality estimate total_estimate0.8727
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary67.4
Skewness Skewness skewness0.274
Kurtosis Kurtosis kurtosis-0.238
Angular range angular_range— – 0.1550 −1
Current regularization parameter α current_alpha0.0002
Highest regularization parameter α highest_alpha488100000.0000
Real-space data points n_real_points32
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.818; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.887

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (20 domains)

Domain ID domain_idd6x1qa1
Class classb — All beta proteins
Fold Fold foldb.18 — Galactose-binding domain-like
Superfamily Superfamily superfamilyb.18.1 — Galactose-binding domain-like
Family Family familyb.18.1.0 — automated matches
Domain ID domain_idd6x1qa2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.4 — beta-Galactosidase/glucuronidase domain
Family Family familyb.1.4.0 — automated matches
Domain ID domain_idd6x1qa3
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.1.8.0 — automated matches
Domain ID domain_idd6x1qa4
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.4 — beta-Galactosidase/glucuronidase domain
Family Family familyb.1.4.0 — automated matches
Domain ID domain_idd6x1qa5
Class classb — All beta proteins
Fold Fold foldb.30 — Supersandwich
Superfamily Superfamily superfamilyb.30.5 — Galactose mutarotase-like
Family Family familyb.30.5.0 — automated matches
Domain ID domain_idd6x1qb1
Class classb — All beta proteins
Fold Fold foldb.18 — Galactose-binding domain-like
Superfamily Superfamily superfamilyb.18.1 — Galactose-binding domain-like
Family Family familyb.18.1.0 — automated matches
Domain ID domain_idd6x1qb2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.4 — beta-Galactosidase/glucuronidase domain
Family Family familyb.1.4.0 — automated matches
Domain ID domain_idd6x1qb3
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.1.8.0 — automated matches
Domain ID domain_idd6x1qb4
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.4 — beta-Galactosidase/glucuronidase domain
Family Family familyb.1.4.0 — automated matches
Domain ID domain_idd6x1qb5
Class classb — All beta proteins
Fold Fold foldb.30 — Supersandwich
Superfamily Superfamily superfamilyb.30.5 — Galactose mutarotase-like
Family Family familyb.30.5.0 — automated matches
Domain ID domain_idd6x1qc1
Class classb — All beta proteins
Fold Fold foldb.18 — Galactose-binding domain-like
Superfamily Superfamily superfamilyb.18.1 — Galactose-binding domain-like
Family Family familyb.18.1.0 — automated matches
Domain ID domain_idd6x1qc2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.4 — beta-Galactosidase/glucuronidase domain
Family Family familyb.1.4.0 — automated matches
Domain ID domain_idd6x1qc3
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.1.8.0 — automated matches
Domain ID domain_idd6x1qc4
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.4 — beta-Galactosidase/glucuronidase domain
Family Family familyb.1.4.0 — automated matches
Domain ID domain_idd6x1qc5
Class classb — All beta proteins
Fold Fold foldb.30 — Supersandwich
Superfamily Superfamily superfamilyb.30.5 — Galactose mutarotase-like
Family Family familyb.30.5.0 — automated matches
Domain ID domain_idd6x1qd1
Class classb — All beta proteins
Fold Fold foldb.18 — Galactose-binding domain-like
Superfamily Superfamily superfamilyb.18.1 — Galactose-binding domain-like
Family Family familyb.18.1.0 — automated matches
Domain ID domain_idd6x1qd2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.4 — beta-Galactosidase/glucuronidase domain
Family Family familyb.1.4.0 — automated matches
Domain ID domain_idd6x1qd3
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.1.8.0 — automated matches
Domain ID domain_idd6x1qd4
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.4 — beta-Galactosidase/glucuronidase domain
Family Family familyb.1.4.0 — automated matches
Domain ID domain_idd6x1qd5
Class classb — All beta proteins
Fold Fold foldb.30 — Supersandwich
Superfamily Superfamily superfamilyb.30.5 — Galactose mutarotase-like
Family Family familyb.30.5.0 — automated matches

8. Citations (1)

9. Files and Curves (10)