6MWF

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
R-Value Work: 0.149
R-Value Observed: 0.151

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

Literature

Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF) Burkholderia pseudomallei in complex with ligand HGN-0456.

Abendroth, J., Dranow, D.M., Pierce, P.G., Horn, J.R., Hagen, T.J., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

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]	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]	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]	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]	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
R-Value Work: 0.149
R-Value Observed: 0.151
Space Group: C 1 2 1
Diffraction Data: https://doi.org/10.18430/m36mwf

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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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

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Help and Resources

6MWF

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

Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF) Burkholderia pseudomallei in complex with ligand HGN-0456.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)