4HA3 | pdb_00004ha3

Structure of beta-glycosidase from Acidilobus saccharovorans in complex with Tris

• PDB DOI: https://doi.org/10.2210/pdb4HA3/pdb

• Classification: HYDROLASE
• Organism(s): Acidilobus saccharovorans 345-15
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-09-25 Released: 2012-10-10 
• Deposition Author(s): Trofimov, A.A., Polyakov, K.M., Tikhonov, A.V., Bezsudnova, E.Y., Dorovatovskii, P.V., Gumerov, V.M., Ravin, N.V., Skryabin, K.G., Popov, V.O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å
• R-Value Free: 
  0.159 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.143 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.144 (Depositor) 

Starting Model: experimental

Literature

Structures of beta-glycosidase from Acidilobus saccharovorans in complexes with tris and glycerol.

Trofimov, A.A., Polyakov, K.M., Tikhonov, A.V., Bezsudnova, E.Y., Dorovatovskii, P.V., Gumerov, V.M., Ravin, N.V., Skryabin, K.G., Popov, V.O.

(null) Dokl Biochem Biophys 449: 99-101

• PubMed: 23657657 
• DOI: https://doi.org/10.1134/S1607672913020129
• Primary Citation of Related Structures:  
  4HA3, 4HA4

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Organizational Affiliation: 

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia. [e-mail]

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 56.08 kDa 
• Atom Count: 4,519 
• Modeled Residue Count: 489 
• Deposited Residue Count: 489 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-galactosidase	A	489	Acidilobus saccharovorans 345-15	Mutation(s): 0  Gene Names: ASAC1390, ASAC_1390 EC: 3.2.1.23
UniProt
Find proteins for D9PZ08 (Acidilobus saccharovorans (strain DSM 16705 / JCM 18335 / VKM B-2471 / 345-15)) Explore D9PZ08  Go to UniProtKB:  D9PZ08

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	B [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
PEG	H [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	C [auth A], D [auth A], E [auth A], G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å
• R-Value Free:  0.159 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.143 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.144 (Depositor) 

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.18	α = 90
b = 84.18	β = 90
c = 166.22	γ = 90

Software Package:

Software Name	Purpose
AUTOMAR	data collection
BALBES	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-10 
Deposition Author(s): Trofimov, A.A., Polyakov, K.M., Tikhonov, A.V., Bezsudnova, E.Y., Dorovatovskii, P.V., Gumerov, V.M., Ravin, N.V., Skryabin, K.G., Popov, V.O.

Revision History  

• Version 1.0: 2012-10-10
  Type: Initial release
  
• Version 1.1: 2013-09-04
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-12-27
  Changes: Derived calculations
• Version 1.4: 2024-11-27
  Changes: Structure summary