9EP0 | pdb_00009ep0

Dolichyl phosphate mannose synthase in complex with donor (GDP-Man) and traces of acceptor (Dol55P) and product (Dol55P-Man)

• PDB DOI: https://doi.org/10.2210/pdb9EP0/pdb

• Classification: TRANSFERASE
• Organism(s): Pyrococcus furiosus DSM 3638
• Expression System: Escherichia coli B
• Mutation(s): No 


• Deposited: 2024-03-16 Released: 2025-10-01 
• Deposition Author(s): Gandini, R., Keskitalo, M.M., Reichenbach, T., Divne, C.
• Funding Organization(s): Swedish Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.301 (Depositor), 0.303 (DCC) 
• R-Value Work: 
  0.237 (Depositor), 0.249 (DCC) 
• R-Value Observed: 
  0.243 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Pyrococcus furiosus dolichylphosphate mannose synthase in complex with substrates (GDP-Man and DolP) and traces of a flipped glycolipid product (DolP-Man)

Gandini, R., Keskitalo, M., Reichenbach, T., Divne, C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 44.45 kDa 
• Atom Count: 2,859 
• Modeled Residue Count: 343 
• Deposited Residue Count: 374 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dolichol monophosphate mannose synthase	A	374	Pyrococcus furiosus DSM 3638	Mutation(s): 0  Gene Names: PF0058 EC: 2.4.1.83
UniProt
Find proteins for Q8U4M3 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8U4M3  Go to UniProtKB:  Q8U4M3

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MJC (Subject of Investigation/LOI)	E [auth A]	dolichyl phosphate mannose C61 H103 O9 P FVCCNKBLEFCPJO-ALFQADJPSA-N
GDD (Subject of Investigation/LOI)	B [auth A]	GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE C16 H25 N5 O16 P2 MVMSCBBUIHUTGJ-GDJBGNAASA-N
EFS (Subject of Investigation/LOI)	D [auth A]	ETHYL DIHYDROGEN PHOSPHATE C2 H7 O4 P ZJXZSIYSNXKHEA-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.301 (Depositor), 0.303 (DCC) 
• R-Value Work:  0.237 (Depositor), 0.249 (DCC) 
• R-Value Observed: 0.243 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.8	α = 90
b = 145.25	β = 90
c = 99.02	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-01 
Deposition Author(s): Gandini, R., Keskitalo, M.M., Reichenbach, T., Divne, C.

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Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	2017-03877
Swedish Research Council	Sweden	2013-5717

Revision History  

• Version 1.0: 2025-10-01
  Type: Initial release