3IMH | pdb_00003imh

CRYSTAL STRUCTURE OF GALACTOSE 1-EPIMERASE FROM Lactobacillus acidophilus NCFM

PDB DOI: https://doi.org/10.2210/pdb3IMH/pdb

Classification: ISOMERASE
Organism(s): Lactobacillus acidophilus NCFM
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2009-08-10 Released: 2009-08-18
Deposition Author(s): Patskovsky, Y., Toro, R., Dickey, M., Chang, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free:
0.170 (Depositor), 0.169 (DCC)
R-Value Work:
0.140 (Depositor), 0.140 (DCC)
R-Value Observed:
0.141 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

Literature

CRYSTAL STRUCTURE OF GALACTOSE 1-EPIMERASE FROM Lactobacillus acidophilus

Patskovsky, Y., Toro, R., Dickey, M., Chang, S., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 77.05 kDa
Atom Count: 6,441
Modeled Residue Count: 664
Deposited Residue Count: 676
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galactose-1-epimerase	A, B	338	Lactobacillus acidophilus NCFM	Mutation(s): 1 Gene Names: galM, LBA1457 EC: 5.1.3.3
UniProt
Find proteins for Q5FJ46 (Lactobacillus acidophilus (strain ATCC 700396 / NCK56 / N2 / NCFM)) Explore Q5FJ46 Go to UniProtKB: Q5FJ46
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5FJ46
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain K [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain K [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain K [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] H [auth A] I [auth A] K [auth A] F [auth A], G [auth A], H [auth A], I [auth A], K [auth A], M [auth B], N [auth B], O [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain J [auth A] SDF format, chain E [auth A] MOL2 format, chain P [auth B] MOL2 format, chain J [auth A] MOL2 format, chain E [auth A] mmCIF format, chain P [auth B] mmCIF format, chain J [auth A] mmCIF format, chain E [auth A]	E [auth A], J [auth A], P [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain J [auth A] Focus chain P [auth B] Interactions & Density Focus chain E [auth A] Focus chain J [auth A] Focus chain P [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain L [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain L [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], L [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain L [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free: 0.170 (Depositor), 0.169 (DCC)
R-Value Work: 0.140 (Depositor), 0.140 (DCC)
R-Value Observed: 0.141 (Depositor)

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.683	α = 90
b = 134.683	β = 90
c = 103.027	γ = 90

Software Package:

Software Name	Purpose
SHELXCD	phasing
SHELXD	phasing
SHELXE	model building
REFMAC	refinement
DENZO	data reduction
HKL-2000	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-08-18

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2009-08-18
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2018-11-21
Changes: Data collection, Structure summary
Version 1.4: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
Version 1.5: 2021-10-13
Changes: Database references
Version 1.6: 2024-02-21
Changes: Data collection