4C8G

IspF (Burkholderia cenocepacia) CMP complex

PDB DOI: https://doi.org/10.2210/pdb4C8G/pdb

Classification: LYASE
Organism(s): Burkholderia cenocepacia J2315
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-10-01 Released: 2014-01-08
Deposition Author(s): O'Rourke, P.E.F., Kalinowska-Tluscik, J., Fyfe, P.K., Dawson, A., Hunter, W.N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.279
R-Value Work: 0.237
R-Value Observed: 0.239

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structures of Ispf from Plasmodium Falciparum and Burkholderia Cenocepacia: Comparisons Inform Antimicrobial Drug Target Assessment.

O'Rourke, P.E.F., Kalinowska-Tluscik, J., Fyfe, P.K., Dawson, A., Hunter, W.N.

(2014) BMC Struct Biol 14: 1

PubMed: 24410837 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1186/1472-6807-14-1
Primary Citation of Related Structures:
4C81, 4C82, 4C8E, 4C8G, 4C8I

PubMed Abstract:
2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase (IspF) catalyzes the conversion of 4-diphosphocytidyl-2C-methyl-D-erythritol-2-phosphate to 2C-methyl-D-erythritol-2,4-cyclodiphosphate and cytidine monophosphate in production of isoprenoid-precursors via the methylerythritol phosphate biosynthetic pathway. IspF is found in the protozoan Plasmodium falciparum, a parasite that causes cerebral malaria, as well as in many Gram-negative bacteria such as Burkholderia cenocepacia. IspF represents a potential target for development of broad-spectrum antimicrobial drugs since it is proven or inferred as essential in these pathogens and absent from mammals. Structural studies of IspF from these two important yet distinct pathogens, and comparisons with orthologues have been carried out to generate reagents, to support and inform a structure-based approach to early stage drug discovery.

Organizational Affiliation

Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK. w.n.hunter@dundee.ac.uk.

Macromolecule Content

Total Structure Weight: 59.21 kDa
Atom Count: 3,757
Modelled Residue Count: 458
Deposited Residue Count: 546
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE	A, B, C	182	Burkholderia cenocepacia J2315	Mutation(s): 0 EC: 4.6.1.12
UniProt
Find proteins for B4EC22 (Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610)) Explore B4EC22 Go to UniProtKB: B4EC22
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B4EC22
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
C5P Query on C5P Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain K [auth C] SDF format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain K [auth C] MOL2 format, chain E [auth A]	E [auth A], G [auth B], K [auth C]	CYTIDINE-5'-MONOPHOSPHATE C₉ H₁₄ N₃ O₈ P IERHLVCPSMICTF-XVFCMESISA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain K [auth C] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain K [auth C]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B]	H [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain D [auth A] SDF format, chain J [auth C] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain J [auth C]	D [auth A], F [auth B], J [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Focus chain J [auth C] Interactions & Density Focus chain D [auth A] Focus chain F [auth B] Focus chain J [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B]	I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.279
R-Value Work: 0.237
R-Value Observed: 0.239
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.23	α = 90
b = 88.552	β = 103.87
c = 72.392	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-01-08

Deposition Author(s):

O'Rourke, P.E.F.

Kalinowska-Tluscik, J.

Fyfe, P.K.

Dawson, A.

Hunter, W.N.

Revision History (Full details and data files)

Version 1.0: 2014-01-08
Type: Initial release
Version 1.1: 2014-01-29
Changes: Database references
Version 1.2: 2019-05-08
Changes: Data collection, Experimental preparation, Other
Version 1.3: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Refinement description