7brs

E.coli beta-galactosidase (E537Q) in complex with fluorescent probe KSA02

Method: X-RAY DIFFRACTION Dmax: 207.4 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 F4X 8-[2-[(E)-2-[4-[(2S,3R,4S,5R,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxyphenyl]ethenyl]-3,3-dimethyl-indol-1-ium-1-yl]octanoic acid × 4 MG MAGNESIUM ION × 8 NA SODIUM ION × 6 DMS DIMETHYL SULFOXIDE × 54 GOL GLYCEROL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;291 K;100mM Bis-Tris, pH=5.9, 200mM NaCl, 200mM MgCl2, 10% PEG8000, 10% glycerol, 0.1M guanidine hydrochloride, 10mM DTT Resolution 2.67 Å R-free 0.244
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 F4X 8-[2-[(E)-2-[4-[(2S,3R,4S,5R,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxyphenyl]ethenyl]-3,3-dimethyl-indol-1-ium-1-yl]octanoic acid × 4 MG MAGNESIUM ION × 8 NA SODIUM ION × 8 DMS DIMETHYL SULFOXIDE × 38 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;291 K;100mM Bis-Tris, pH=5.9, 200mM NaCl, 200mM MgCl2, 10% PEG8000, 10% glycerol, 0.1M guanidine hydrochloride, 10mM DTT Resolution 2.67 Å R-free 0.244

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 7brs

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7brs
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7brs
Deposition date deposition_date2020-03-30
Structure title titleE.coli beta-galactosidase (E537Q) in complex with fluorescent probe KSA02
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_guinier61.89
Radius of gyration Rg (electron density) rg_electron62.46
Forward intensity I(0) i03066810000.00
Molecular weight molecular_weight455030.0 kDa
Excluded volume excluded_volume563220 ų
Envelope volume envelope_volume770350 ų
Hydration-shell volume shell_volume106040 ų
Envelope diameter envelope_diameter234.3
Shell Rg shell_rg60.99
Envelope Rg envelope_rg61.62
Shape Rg shape_rg62.42
Total Rg total_rg62.57
Total atoms total_atoms32096
Residues n_residues4063
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 dmax207.4
Rg (real space) rg_real62.32
Rg uncertainty (real space) rg_real_error1.74
I(0) (real space) i0_real3.0640e+09
I(0) uncertainty (real space) i0_real_error6.0050e+07
Rg (reciprocal space) rg_reciprocal61.37
I(0) (reciprocal space) i0_reciprocal3061000000.0000
Solution quality estimate total_estimate0.8518
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary66.4
Skewness Skewness skewness0.552
Kurtosis Kurtosis kurtosis-0.081
Angular range angular_range— – 0.1250 −1
Current regularization parameter α current_alpha0.0034
Highest regularization parameter α highest_alpha162000000.0000
Real-space data points n_real_points26
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.853; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.518

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_idd7brsa1
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_idd7brsa2
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_idd7brsa3
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_idd7brsa4
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_idd7brsa5
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_idd7brsb1
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_idd7brsb2
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_idd7brsb3
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_idd7brsb4
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_idd7brsb5
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_idd7brsc1
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_idd7brsc2
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_idd7brsc3
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_idd7brsc4
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_idd7brsc5
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_idd7brsd1
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_idd7brsd2
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_idd7brsd3
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_idd7brsd4
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_idd7brsd5
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)