7btk

E.coli beta-galactosidase (E537Q) in complex with fluorescent probe KSA01

Method: X-RAY DIFFRACTION Dmax: 209.1 Å Quality: GOOD

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

Beta-galactosidase

Escherichia coli K-12

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 1–1024 Chain C; UniProt 1–1024 Mutation:E537Q F6L 4-[[2-[(E)-2-[4-[(2S,3R,4S,5R,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxyphenyl]ethenyl]-3,3-dimethyl-2H-indol-1-yl]methyl]benzoic acid × 4 MG MAGNESIUM ION × 8 NA SODIUM ION × 8 DMS DIMETHYL SULFOXIDE × 40 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;291 K;100 mM Bis-Tris, pH = 5.9, 200 mM NaCl, 200 mM MgCl2, 10% PEG8000, 10% glycerol, 0.1 M guanidine hydrochloride and 10 mM DTT Resolution 2.70 Å R-free 0.233
2 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain B; UniProt 1–1024 Chain D; UniProt 1–1024 Mutation:E537Q F6L 4-[[2-[(E)-2-[4-[(2S,3R,4S,5R,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxyphenyl]ethenyl]-3,3-dimethyl-2H-indol-1-yl]methyl]benzoic acid × 4 MG MAGNESIUM ION × 6 NA SODIUM ION × 6 DMS DIMETHYL SULFOXIDE × 36 GOL GLYCEROL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;291 K;100 mM Bis-Tris, pH = 5.9, 200 mM NaCl, 200 mM MgCl2, 10% PEG8000, 10% glycerol, 0.1 M guanidine hydrochloride and 10 mM DTT Resolution 2.70 Å R-free 0.233

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 82 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 2–1025; UniProt 1–1024 Author chain B; PDBConstruct 2–1025; UniProt 1–1024 Author chain C; PDBConstruct 2–1025; UniProt 1–1024 Author chain D; PDBConstruct 2–1025; UniProt 1–1024

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 7btk

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7btk
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id7btk
Deposition date deposition_date2020-04-01
Structure title titleE.coli beta-galactosidase (E537Q) in complex with fluorescent probe KSA01
Keywords keywordsbeta_galactosidase, fluorescent probe, hydrolase; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier62.41
Radius of gyration Rg (electron density) rg_electron62.94
Forward intensity I(0) i03160360000.00
Molecular weight molecular_weight464190.0 kDa
Excluded volume excluded_volume575620 ų
Envelope volume envelope_volume790190 ų
Hydration-shell volume shell_volume107740 ų
Envelope diameter envelope_diameter242.3
Shell Rg shell_rg61.56
Envelope Rg envelope_rg62.14
Shape Rg shape_rg62.91
Total Rg total_rg63.02
Total atoms total_atoms32738
Residues n_residues4086
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 dmax209.1
Rg (real space) rg_real62.82
Rg uncertainty (real space) rg_real_error1.57
I(0) (real space) i0_real3.1570e+09
I(0) uncertainty (real space) i0_real_error5.8250e+07
Rg (reciprocal space) rg_reciprocal61.88
I(0) (reciprocal space) i0_reciprocal3154000000.0000
Solution quality estimate total_estimate0.8538
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary75.3
Skewness Skewness skewness0.550
Kurtosis Kurtosis kurtosis-0.073
Angular range angular_range— – 0.1250 −1
Current regularization parameter α current_alpha0.0055
Highest regularization parameter α highest_alpha183400000.0000
Real-space data points n_real_points26
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.855; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.537

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (20 domains)

Domain ID domain_idd7btka1
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.18.1.5 — beta-Galactosidase/glucuronidase, N-terminal domain
Domain ID domain_idd7btka2
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.1.4.1 — beta-Galactosidase/glucuronidase domain
Domain ID domain_idd7btka3
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.1.8.3 — beta-glycanases
Domain ID domain_idd7btka4
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.1.4.1 — beta-Galactosidase/glucuronidase domain
Domain ID domain_idd7btka5
Class classb — All beta proteins
Fold Fold foldb.30 — Supersandwich
Superfamily Superfamily superfamilyb.30.5 — Galactose mutarotase-like
Family Family familyb.30.5.1 — beta-Galactosidase, domain 5
Domain ID domain_idd7btkb1
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.18.1.5 — beta-Galactosidase/glucuronidase, N-terminal domain
Domain ID domain_idd7btkb2
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.1.4.1 — beta-Galactosidase/glucuronidase domain
Domain ID domain_idd7btkb3
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.1.8.3 — beta-glycanases
Domain ID domain_idd7btkb4
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.1.4.1 — beta-Galactosidase/glucuronidase domain
Domain ID domain_idd7btkb5
Class classb — All beta proteins
Fold Fold foldb.30 — Supersandwich
Superfamily Superfamily superfamilyb.30.5 — Galactose mutarotase-like
Family Family familyb.30.5.1 — beta-Galactosidase, domain 5
Domain ID domain_idd7btkc1
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.18.1.5 — beta-Galactosidase/glucuronidase, N-terminal domain
Domain ID domain_idd7btkc2
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.1.4.1 — beta-Galactosidase/glucuronidase domain
Domain ID domain_idd7btkc3
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.1.8.3 — beta-glycanases
Domain ID domain_idd7btkc4
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.1.4.1 — beta-Galactosidase/glucuronidase domain
Domain ID domain_idd7btkc5
Class classb — All beta proteins
Fold Fold foldb.30 — Supersandwich
Superfamily Superfamily superfamilyb.30.5 — Galactose mutarotase-like
Family Family familyb.30.5.1 — beta-Galactosidase, domain 5
Domain ID domain_idd7btkd1
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.18.1.5 — beta-Galactosidase/glucuronidase, N-terminal domain
Domain ID domain_idd7btkd2
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.1.4.1 — beta-Galactosidase/glucuronidase domain
Domain ID domain_idd7btkd3
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.1.8.3 — beta-glycanases
Domain ID domain_idd7btkd4
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.1.4.1 — beta-Galactosidase/glucuronidase domain
Domain ID domain_idd7btkd5
Class classb — All beta proteins
Fold Fold foldb.30 — Supersandwich
Superfamily Superfamily superfamilyb.30.5 — Galactose mutarotase-like
Family Family familyb.30.5.1 — beta-Galactosidase, domain 5

8. Citations (1)

9. Files and Curves (10)