3W5G | pdb_00003w5g

Crystal structure of tomato beta-galactosidase 4 in complex with galactose

• PDB DOI: https://doi.org/10.2210/pdb3W5G/pdb

• Classification: HYDROLASE
• Organism(s): Solanum lycopersicum
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2013-01-29 Released: 2014-01-29 
• Deposition Author(s): Eda, M., Tada, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.259 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of tomato beta-galactosidase 4 in complex with galactose

Eda, M., Tada, T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 162.1 kDa 
• Atom Count: 11,426 
• Modeled Residue Count: 1,410 
• Deposited Residue Count: 1,436 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-galactosidase	A, B	718	Solanum lycopersicum	Mutation(s): 0  Gene Names: TBG4 EC: 3.2.1.23
UniProt
Find proteins for O81100 (Solanum lycopersicum) Explore O81100  Go to UniProtKB:  O81100
Glycosylation
Glycosylation Sites: 2

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth A], E [auth A], K [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GAL	F [auth A], G [auth A], H [auth A], I [auth A], J [auth B], L [auth B], M [auth B], N [auth B]	beta-D-galactopyranose C6 H12 O6 WQZGKKKJIJFFOK-FPRJBGLDSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.259 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.93	α = 90
b = 106.382	β = 90
c = 162.379	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-01-29 
Deposition Author(s): Eda, M., Tada, T.

Revision History  

• Version 1.0: 2014-01-29
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-11-20
  Changes: Structure summary