6MWF | pdb_00006mwf

Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF) Burkholderia pseudomallei in complex with ligand HGN-0459

PDB DOI: https://doi.org/10.2210/pdb6MWF/pdb

Classification: LYASE
Organism(s): Burkholderia pseudomallei 1710b
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-10-29 Released: 2019-11-06
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.184 (Depositor), 0.180 (DCC)
R-Value Work:
0.149 (Depositor), 0.150 (DCC)
R-Value Observed:
0.151 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Analysis of Burkholderia pseudomallei IspF in complex with sulfapyridine, sulfamonomethoxine, ethoxzolamide and acetazolamide

Grote, D., Stewart, C.G., Daraji, D.G., Enayati, P., Braverman, K.N., Romanaggi, C., Bolejack, M.J., Yano, J.K., Abendroth, J., Dranow, D.M., Pierce, P.G., Lorimer, D.D., Horanyi, P.S., Staker, B.L., Edwards, T.E., Myler, P.J., Horn, J.R., Hagen, T.J.

(2025) Acta Crystallogr F Struct Biol Commun 81: 138-145

Macromolecule Content

Total Structure Weight: 53.32 kDa
Atom Count: 4,054
Modelled Residue Count: 474
Deposited Residue Count: 498
Unique protein chains: 1

Macromolecules

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(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	166	Burkholderia pseudomallei 1710b	Mutation(s): 0 Gene Names: ispF, BURPS1710b_2511 EC: 4.6.1.12
UniProt
Find proteins for Q3JRA0 (Burkholderia pseudomallei (strain 1710b)) Explore Q3JRA0 Go to UniProtKB: Q3JRA0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q3JRA0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SFY (Subject of Investigation/LOI) Query on SFY Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth C] MOL2 format, chain E [auth A] MOL2 format, chain J [auth C] mmCIF format, chain E [auth A] mmCIF format, chain J [auth C]	E [auth A], J [auth C]	4-amino-N-(pyridin-2-yl)benzenesulfonamide C₁₁ H₁₁ N₃ O₂ S GECHUMIMRBOMGK-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth C] Interactions & Density Focus chain E [auth A] Focus chain J [auth C]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] SDF format, chain I [auth C] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth C] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth C]	D [auth A], H [auth B], I [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Focus chain I [auth C] Interactions & Density Focus chain D [auth A] Focus chain H [auth B] Focus chain I [auth C]
ACT Query on ACT 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]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.184 (Depositor), 0.180 (DCC)
R-Value Work: 0.149 (Depositor), 0.150 (DCC)
R-Value Observed: 0.151 (Depositor)

Diffraction Data: https://doi.org/10.18430/m36mwf

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.03	α = 90
b = 67.93	β = 96.58
c = 60.76	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2019-11-06

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2019-11-06
Type: Initial release
Version 1.1: 2019-11-20
Changes: Database references
Version 1.2: 2020-03-11
Changes: Data collection
Version 1.3: 2023-10-11
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2025-04-09
Changes: Database references, Structure summary

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Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF) Burkholderia pseudomallei in complex with ligand HGN-0459

Analysis of Burkholderia pseudomallei IspF in complex with sulfapyridine, sulfamonomethoxine, ethoxzolamide and acetazolamide

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations