6H93 | pdb_00006h93

Beta-phosphoglucomutase from Lactococcus lactis with inorganic phosphate bound in an open conformer to 1.8 A.

PDB DOI: https://doi.org/10.2210/pdb6H93/pdb

Classification: ISOMERASE
Organism(s): Lactococcus lactis subsp. lactis Il1403
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2018-08-03 Released: 2020-08-26
Deposition Author(s): Robertson, A.J., Bisson, C., Waltho, J.P.
Funding Organization(s): Biotechnology and Biological Sciences Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free:
0.233 (Depositor), 0.240 (DCC)
R-Value Work:
0.179 (Depositor), 0.190 (DCC)
R-Value Observed:
0.182 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Transition state of phospho-enzyme hydrolysis in beta-phosphoglucomutase.

Robertson, A.J., Bisson, C., Waltho, J.P.

To be published.

Macromolecule Content

Total Structure Weight: 49.35 kDa
Atom Count: 3,721
Modeled Residue Count: 438
Deposited Residue Count: 442
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-phosphoglucomutase	A, B	221	Lactococcus lactis subsp. lactis Il1403	Mutation(s): 2 Gene Names: pgmB, LL0429, L0001 EC: 5.4.2.6
UniProt
Find proteins for P71447 (Lactococcus lactis subsp. lactis (strain IL1403)) Explore P71447 Go to UniProtKB: P71447
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P71447
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain P [auth B] MOL2 format, chain I [auth A] MOL2 format, chain P [auth B] mmCIF format, chain I [auth A] mmCIF format, chain P [auth B]	I [auth A], P [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain I [auth A] Focus chain P [auth B] Interactions & Density Focus chain I [auth A] Focus chain P [auth B]
PDO Query on PDO Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	1,3-PROPANDIOL C₃ H₈ O₂ YPFDHNVEDLHUCE-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B]	D [auth A] E [auth A] F [auth A] L [auth B] M [auth B] D [auth A], E [auth A], F [auth A], L [auth B], M [auth B], N [auth B], O [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	G [auth A], H [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain K [auth B] MOL2 format, chain C [auth A] MOL2 format, chain K [auth B] mmCIF format, chain C [auth A] mmCIF format, chain K [auth B]	C [auth A], K [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free: 0.233 (Depositor), 0.240 (DCC)
R-Value Work: 0.179 (Depositor), 0.190 (DCC)
R-Value Observed: 0.182 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.35	α = 90
b = 117.14	β = 99.14
c = 53.19	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
Coot	model building
MOLREP	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-08-26

Deposition Author(s):

Robertson, A.J.

Bisson, C.

Waltho, J.P.

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/M021637/1
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/K016245/1