4GM6

Crystal structure of PfkB family carbohydrate kinase(TARGET EFI-502146 FROM Listeria grayi DSM 20601

PDB DOI: https://doi.org/10.2210/pdb4GM6/pdb

Classification: TRANSFERASE
Organism(s): Listeria grayi DSM 20601
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-08-15 Released: 2012-09-26
Deposition Author(s): Patskovsky, Y., Toro, R., Bhosle, R., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Zencheck, W.D., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.218
R-Value Work: 0.175
R-Value Observed: 0.176

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of PfkB family carbohydrate kinase FROM Listeria grayi

Patskovsky, Y., Toro, R., Bhosle, R., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Zencheck, W.D., Imker, H.J., Gerlt, J.A., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 236.76 kDa
Atom Count: 16,449
Modelled Residue Count: 1,927
Deposited Residue Count: 2,106
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PfkB family carbohydrate kinase	A, B, C, D, E A, B, C, D, E, F	351	Listeria grayi DSM 20601	Mutation(s): 0 Gene Names: HMPREF0556_10677
UniProt
Find proteins for D7UWR6 (Listeria grayi DSM 20601) Explore D7UWR6 Go to UniProtKB: D7UWR6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D7UWR6
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.218
R-Value Work: 0.175
R-Value Observed: 0.176
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.832	α = 90
b = 109.862	β = 101.92
c = 109.592	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2012-09-26

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2012-09-26
Type: Initial release
Version 1.1: 2018-01-24
Changes: Structure summary
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description