1jz8

E. COLI (lacZ) BETA-GALACTOSIDASE (E537Q) IN COMPLEX WITH ALLOLACTOSE

Method: X-RAY DIFFRACTION Dmax: 174.3 Å Quality: GOOD

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

Beta-Galactosidase

Escherichia coli

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 Other combination Homooligomer Protein × 4 其他Polymer 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 1–1023 Chain B; UniProt 1–1023 Chain C; UniProt 1–1023 Chain D; UniProt 1–1023 Mutation:E537Q beta-D-galactopyranose-(1-6)-beta-D-glucopyranose × 4 MG MAGNESIUM ION × 16 NA SODIUM ION × 16 DMS DIMETHYL SULFOXIDE × 127 BGC beta-D-glucopyranose × 1 TAR D(-)-TARTARIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;288 K;Bis-Tris, PEG 8000, MgCl2, NaCl, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP at 288K, pH 6.50 Resolution 1.50 Å R-free 0.208

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 1–1023; UniProt 1–1023 Author chain B; PDBConstruct 1–1023; UniProt 1–1023 Author chain C; PDBConstruct 1–1023; UniProt 1–1023 Author chain D; PDBConstruct 1–1023; UniProt 1–1023

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 1jz8

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1jz8
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1jz8
Deposition date deposition_date2001-09-13
Structure title titleE. COLI (lacZ) BETA-GALACTOSIDASE (E537Q) IN COMPLEX WITH ALLOLACTOSE
Keywords keywordsTIM BARREL (ALPHA/BETA BARREL), JELLY-ROLL BARREL, IMMUNOGLOBULIN, BETA SUPERSANDWICH, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier52.02
Radius of gyration Rg (electron density) rg_electron51.68
Forward intensity I(0) i03333170000.00
Molecular weight molecular_weight472140.0 kDa
Excluded volume excluded_volume584480 ų
Envelope volume envelope_volume753790 ų
Hydration-shell volume shell_volume116250 ų
Envelope diameter envelope_diameter184.4
Shell Rg shell_rg59.12
Envelope Rg envelope_rg51.14
Shape Rg shape_rg51.68
Total Rg total_rg51.86
Total atoms total_atoms33132
Residues n_residues4044
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 dmax174.3
Rg (real space) rg_real51.93
Rg uncertainty (real space) rg_real_error1.56
I(0) (real space) i0_real3.3330e+09
I(0) uncertainty (real space) i0_real_error6.2280e+07
Rg (reciprocal space) rg_reciprocal52.09
I(0) (reciprocal space) i0_reciprocal3334000000.0000
Solution quality estimate total_estimate0.8688
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary63.9
Skewness Skewness skewness0.309
Kurtosis Kurtosis kurtosis-0.179
Angular range angular_range— – 0.1500 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha505600000.0000
Real-space data points n_real_points31
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.832; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.972; Smooth: 0.824

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (8)

7. Fold Classification (SCOP + CATH) 40 domains

SCOP 2.08 (20 domains)

Domain ID domain_idd1jz8a1
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_idd1jz8a2
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_idd1jz8a3
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_idd1jz8a4
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_idd1jz8a5
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_idd1jz8b1
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_idd1jz8b2
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_idd1jz8b3
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_idd1jz8b4
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_idd1jz8b5
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_idd1jz8c1
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_idd1jz8c2
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_idd1jz8c3
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_idd1jz8c4
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_idd1jz8c5
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_idd1jz8d1
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_idd1jz8d2
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_idd1jz8d3
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_idd1jz8d4
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_idd1jz8d5
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

CATH v4.4 (20 domains)

Domain ID domain_id1jz8A01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily260 — Galactose-binding domain-like
Domain ID domain_id1jz8A02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1jz8A03
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily80 — Glycosidases
Domain ID domain_id1jz8A04
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1jz8A05
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology98 — Beta-galactosidase; Chain A, domain 5
Homologous superfamily homologous superfamily10
Domain ID domain_id1jz8B01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily260 — Galactose-binding domain-like
Domain ID domain_id1jz8B02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1jz8B03
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily80 — Glycosidases
Domain ID domain_id1jz8B04
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1jz8B05
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology98 — Beta-galactosidase; Chain A, domain 5
Homologous superfamily homologous superfamily10
Domain ID domain_id1jz8C01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily260 — Galactose-binding domain-like
Domain ID domain_id1jz8C02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1jz8C03
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily80 — Glycosidases
Domain ID domain_id1jz8C04
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1jz8C05
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology98 — Beta-galactosidase; Chain A, domain 5
Homologous superfamily homologous superfamily10
Domain ID domain_id1jz8D01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily260 — Galactose-binding domain-like
Domain ID domain_id1jz8D02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1jz8D03
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily80 — Glycosidases
Domain ID domain_id1jz8D04
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1jz8D05
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology98 — Beta-galactosidase; Chain A, domain 5
Homologous superfamily homologous superfamily10

8. Citations (5)

9. Files and Curves (10)