4BZF | pdb_00004bzf

Crystal structure of galactose mutarotase GalM from Bacillus subtilis with trehalose

PDB DOI: https://doi.org/10.2210/pdb4BZF/pdb

Classification: ISOMERASE
Organism(s): Bacillus subtilis subsp. subtilis str. 168
Expression System: Escherichia coli K-12
Mutation(s): No

Deposited: 2013-07-25 Released: 2014-08-13
Deposition Author(s): Vanden Broeck, A., Sauvage, E., Herman, R., Kerff, F., Duez, C., Charlier, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.238 (Depositor), 0.237 (DCC)
R-Value Work:
0.194 (Depositor), 0.194 (DCC)
R-Value Observed:
0.197 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

Crystal Structure of Galactose Mutarotase Galm from Bacillus Subtilis with Trehalose

Vanden Broeck, A., Sauvage, E., Herman, R., Kerff, F., Duez, C., Charlier, P.

To be published.

Macromolecule Content

Total Structure Weight: 75.57 kDa
Atom Count: 5,959
Modeled Residue Count: 645
Deposited Residue Count: 648
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALDOSE 1-EPIMERASE	A, B	324	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0 Gene Names: GALM EC: 5.1.3.3
UniProt
Find proteins for P39840 (Bacillus subtilis (strain 168)) Explore P39840 Go to UniProtKB: P39840
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P39840
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose	C, D	2		N/A	Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D
Glycosylation Resources
GlyTouCan: G92130SN GlyCosmos: G92130SN

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth B]	F [auth A], G [auth B]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth B]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900006 Query on PRD_900006	C, D	trehalose	Oligosaccharide / Nutrient		Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.238 (Depositor), 0.237 (DCC)
R-Value Work: 0.194 (Depositor), 0.194 (DCC)
R-Value Observed: 0.197 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.19	α = 90
b = 83.322	β = 90
c = 124.446	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-08-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-08-13
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary
Version 2.1: 2023-12-20
Changes: Data collection, Database references, Refinement description, Structure summary