6HDL | pdb_00006hdl

R49K variant of beta-phosphoglucomutase from Lactococcus lactis complexed with magnesium trifluoride and beta-G6P to 1.2 A.

PDB DOI: https://doi.org/10.2210/pdb6HDL/pdb

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

Deposited: 2018-08-17 Released: 2020-08-26
Deposition Author(s): Wood, H.P., 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: 1.16 Å
R-Value Free:
0.164 (Depositor), 0.160 (DCC)
R-Value Work:
0.132 (Depositor), 0.130 (DCC)
R-Value Observed:
0.134 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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: 24.72 kDa
Atom Count: 2,082
Modeled Residue Count: 219
Deposited Residue Count: 221
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-phosphoglucomutase	A	221	Lactococcus lactis subsp. lactis Il1403	Mutation(s): 3 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P71447
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BG6 (Subject of Investigation/LOI) Query on BG6 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	6-O-phosphono-beta-D-glucopyranose C₆ H₁₃ O₉ P NBSCHQHZLSJFNQ-VFUOTHLCSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MGF (Subject of Investigation/LOI) Query on MGF Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	TRIFLUOROMAGNESATE F₃ Mg GJOMWUHGUQLOAC-UHFFFAOYSA-K		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	E [auth A], F [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
NA Query on NA 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]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.16 Å
R-Value Free: 0.164 (Depositor), 0.160 (DCC)
R-Value Work: 0.132 (Depositor), 0.130 (DCC)
R-Value Observed: 0.134 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.55	α = 90
b = 54.3	β = 90
c = 104.2	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-08-26

Deposition Author(s):

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