2ZU9 | pdb_00002zu9

Crystal structure of mannosyl-3-phosphoglycerate synthase from Pyrococcus horikoshii

• PDB DOI: https://doi.org/10.2210/pdb2ZU9/pdb

• Classification: TRANSFERASE
• Organism(s): Pyrococcus horikoshii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-10-14 Released: 2009-10-27 
• Deposition Author(s): Kawamura, T., Watanabe, N., Tanaka, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.256 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.225 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of mannosyl-3-phosphoglycerate synthase from Pyrococcus horikoshii

Kawamura, T., Watanabe, N., Tanaka, I.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 92.96 kDa 
• Atom Count: 5,961 
• Modeled Residue Count: 728 
• Deposited Residue Count: 788 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mannosyl-3-phosphoglycerate synthase	A, B	394	Pyrococcus horikoshii	Mutation(s): 0  Gene Names: PH0927 EC: 2.4.1.217
UniProt
Find proteins for O58689 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58689  Go to UniProtKB:  O58689

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	C [auth A], D [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
CO	E [auth A], F [auth B]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.256 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.225 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.655	α = 90
b = 84.867	β = 102
c = 83.565	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-27 
Deposition Author(s): Kawamura, T., Watanabe, N., Tanaka, I.

Revision History  

• Version 1.0: 2009-10-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-11-15
  Changes: Data collection
• Version 1.4: 2024-11-20
  Changes: Structure summary