6kuz

E.coli beta-galactosidase (E537Q) in complex with fluorescent probe KSL01

Method: X-RAY DIFFRACTION Dmax: 208.7 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 B; UniProt 1–1024 Mutation:E537Q DVL 3-(1,3-benzothiazol-2-yl)-2-[[4-[(2~{S},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxyphenyl]methoxy]-5-methyl-benzaldehyde × 4 NA SODIUM ION × 12 DMS DIMETHYL SULFOXIDE × 42 MG MAGNESIUM ION × 8 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.9;291 K;10% PEG8000, 100mM Bis-Tris ph5,9, 200mM Nacl, 10mM DTT, 0.1M Guanidine Hydrochloride 10% glycerol Resolution 2.83 Å R-free 0.224
2 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain C; UniProt 1–1024 Chain D; UniProt 1–1024 Mutation:E537Q DVL 3-(1,3-benzothiazol-2-yl)-2-[[4-[(2~{S},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxyphenyl]methoxy]-5-methyl-benzaldehyde × 4 NA SODIUM ION × 12 DMS DIMETHYL SULFOXIDE × 28 MG MAGNESIUM ION × 8 GOL GLYCEROL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.9;291 K;10% PEG8000, 100mM Bis-Tris ph5,9, 200mM Nacl, 10mM DTT, 0.1M Guanidine Hydrochloride 10% glycerol Resolution 2.83 Å R-free 0.224

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 1–1024; UniProt 1–1024 Author chain B; PDBConstruct 1–1024; UniProt 1–1024 Author chain C; PDBConstruct 1–1024; UniProt 1–1024 Author chain D; PDBConstruct 1–1024; 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 6kuz

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id6kuz
Deposition date deposition_date2019-09-03
Structure title titleE.coli beta-galactosidase (E537Q) in complex with fluorescent probe KSL01
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_guinier62.27
Radius of gyration Rg (electron density) rg_electron62.80
Forward intensity I(0) i03150080000.00
Molecular weight molecular_weight463840.0 kDa
Excluded volume excluded_volume575340 ų
Envelope volume envelope_volume792620 ų
Hydration-shell volume shell_volume108060 ų
Envelope diameter envelope_diameter238.6
Shell Rg shell_rg61.51
Envelope Rg envelope_rg62.14
Shape Rg shape_rg62.77
Total Rg total_rg62.84
Total atoms total_atoms32708
Residues n_residues4082
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 dmax208.7
Rg (real space) rg_real62.68
Rg uncertainty (real space) rg_real_error2.00
I(0) (real space) i0_real3.1470e+09
I(0) uncertainty (real space) i0_real_error6.6880e+07
Rg (reciprocal space) rg_reciprocal61.76
I(0) (reciprocal space) i0_reciprocal3144000000.0000
Solution quality estimate total_estimate0.8544
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary75.1
Skewness Skewness skewness0.547
Kurtosis Kurtosis kurtosis-0.076
Angular range angular_range— – 0.1250 −1
Current regularization parameter α current_alpha0.0050
Highest regularization parameter α highest_alpha181200000.0000
Real-space data points n_real_points26
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.856; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.540

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_idd6kuza1
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_idd6kuza2
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_idd6kuza3
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_idd6kuza4
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_idd6kuza5
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_idd6kuzb1
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_idd6kuzb2
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_idd6kuzb3
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_idd6kuzb4
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_idd6kuzb5
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_idd6kuzc1
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_idd6kuzc2
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_idd6kuzc3
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_idd6kuzc4
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_idd6kuzc5
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_idd6kuzd1
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_idd6kuzd2
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_idd6kuzd3
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_idd6kuzd4
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_idd6kuzd5
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)