4HA4 | pdb_00004ha4

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

PDB DOI: https://doi.org/10.2210/pdb4HA4/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.37 Å
R-Value Free:
0.163 (Depositor), 0.162 (DCC)
R-Value Work:
0.130 (Depositor), 0.130 (DCC)
R-Value Observed:
0.132 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1134/S1607672913020129
Primary Citation Related Structures:
4HA3, 4HA4

Organizational Affiliation

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia. burayatina@gmail.com

Macromolecule Content

Total Structure Weight: 57.5 kDa
Atom Count: 4,606
Modeled Residue Count: 489
Deposited Residue Count: 489
Unique protein chains: 1

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D9PZ08
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG6 Query on PG6 Download:Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE C₁₂ H₂₆ O₆ DMDPGPKXQDIQQG-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] I [auth A] J [auth A] L [auth A] G [auth A], H [auth A], I [auth A], J [auth A], L [auth A], M [auth A], N [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A]
SIN Query on SIN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SUCCINIC ACID C₄ H₆ O₄ KDYFGRWQOYBRFD-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], F [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.37 Å
R-Value Free: 0.163 (Depositor), 0.162 (DCC)
R-Value Work: 0.130 (Depositor), 0.130 (DCC)
R-Value Observed: 0.132 (Depositor)

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.12	α = 90
b = 84.12	β = 90
c = 166.27	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-10-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-10-10
Type: Initial release
Version 1.1: 2013-09-04
Changes: Database references
Version 1.2: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary