4UNI

beta-(1,6)-galactosidase from Bifidobacterium animalis subsp. lactis Bl-04 in complex with galactose

PDB DOI: https://doi.org/10.2210/pdb4UNI/pdb

Classification: HYDROLASE
Organism(s): Bifidobacterium animalis subsp. lactis Bl-04
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-05-28 Released: 2014-10-15
Deposition Author(s): Viborg, A.H., Fredslund, F., Katayama, T., Nielsen, S.K., Svensson, B., Kitaoka, M., Lo Leggio, L., Abou Hachem, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.234
R-Value Work: 0.175
R-Value Observed: 0.177

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 3.2 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 237.22 kDa
Atom Count: 16,898
Modelled Residue Count: 2,064
Deposited Residue Count: 2,085
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-GALACTOSIDASE	A, B, C	695	Bifidobacterium animalis subsp. lactis Bl-04	Mutation(s): 0 EC: 3.2.1.23
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GAL Query on GAL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain K [auth B] SDF format, chain N [auth C] MOL2 format, chain D [auth A] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C]	D [auth A], K [auth B], N [auth C]	beta-D-galactopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-FPRJBGLDSA-N		Interactions Focus chain D [auth A] Focus chain K [auth B] Focus chain N [auth C] Interactions & Density Focus chain D [auth A] Focus chain K [auth B] Focus chain N [auth C]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain Q [auth C] SDF format, chain T [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain T [auth C]	E [auth A] F [auth A] G [auth A] L [auth B] Q [auth C] E [auth A], F [auth A], G [auth A], L [auth B], Q [auth C], T [auth C]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain T [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain T [auth C]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain P [auth C] SDF format, chain R [auth C] SDF format, chain S [auth C] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain P [auth C] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C]	H [auth A] I [auth A] M [auth B] P [auth C] R [auth C] H [auth A], I [auth A], M [auth B], P [auth C], R [auth C], S [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain R [auth C] Focus chain S [auth C] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain R [auth C] Focus chain S [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A]	J [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain O [auth C] MOL2 format, chain O [auth C]	O [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain O [auth C] Interactions & Density Focus chain O [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.234
R-Value Work: 0.175
R-Value Observed: 0.177
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.52	α = 90
b = 199.44	β = 90
c = 217.75	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-10-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-10-15
Type: Initial release
Version 2.0: 2018-01-17
Changes: Atomic model, Data collection
Version 3.0: 2019-02-27
Changes: Atomic model, Data collection, Database references
Version 3.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Other, Structure summary
Version 3.2: 2024-01-10
Changes: Data collection, Database references, Refinement description, Structure summary