5DMY | pdb_00005dmy

Beta-galactosidase - construct 33-930

PDB DOI: https://doi.org/10.2210/pdb5DMY/pdb

Classification: HYDROLASE
Organism(s): Bifidobacterium bifidum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-09-09 Released: 2016-10-05
Deposition Author(s): Watson, K.A., Lazidou, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.264 (Depositor), 0.272 (DCC)
R-Value Work:
0.198 (Depositor), 0.210 (DCC)
R-Value Observed:
0.202 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Rational protein engineering toward the development of a beta-galactosidase with improved functional properties

Lazidou, A., Charalampopoulos, D., Watson, K.A.

To be published.

Macromolecule Content

Total Structure Weight: 294.57 kDa
Atom Count: 21,901
Modeled Residue Count: 2,568
Deposited Residue Count: 2,712
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-galactosidase	A, B, C	904	Bifidobacterium bifidum	Mutation(s): 0 Gene Names: bbgIII EC: 3.2.1.23
UniProt
Find proteins for D4QAP3 (Bifidobacterium bifidum) Explore D4QAP3 Go to UniProtKB: D4QAP3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D4QAP3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A], I [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A]
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth C] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth C]	D [auth A], E [auth A], J [auth B], K [auth B], L [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth C]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain N [auth C] SDF format, chain M [auth C] MOL2 format, chain F [auth A] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] mmCIF format, chain F [auth A] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C]	F [auth A], M [auth C], N [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain M [auth C] Focus chain N [auth C] Interactions & Density Focus chain F [auth A] Focus chain M [auth C] Focus chain N [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.264 (Depositor), 0.272 (DCC)
R-Value Work: 0.198 (Depositor), 0.210 (DCC)
R-Value Observed: 0.202 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 153.04	α = 90
b = 52.65	β = 91.64
c = 153.329	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-10-05

Deposition Author(s):

Watson, K.A.

Lazidou, A.

Revision History (Full details and data files)

Version 1.0: 2016-10-05
Type: Initial release
Version 1.1: 2024-05-01
Changes: Data collection, Database references, Derived calculations, Refinement description