3U4G | pdb_00003u4g

The Structure of CobT from Pyrococcus horikoshii

• PDB DOI: https://doi.org/10.2210/pdb3U4G/pdb

• Classification: TRANSFERASE
• Organism(s): Pyrococcus horikoshii OT3
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-10-07 Released: 2011-12-21 
• Deposition Author(s): Cuff, M.E., Evdokimova, E., Mursleen, A., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.216 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.169 (Depositor) 
• R-Value Observed: 
  0.171 (Depositor) 

Literature

The Structure of CobT from Pyrococcus horikoshii

Cuff, M.E., Evdokimova, E., Mursleen, A., Savchenko, A., Edwards, A., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 36.96 kDa 
• Atom Count: 2,719 
• Modeled Residue Count: 326 
• Deposited Residue Count: 337 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NaMN:DMB phosphoribosyltransferase	A	337	Pyrococcus horikoshii OT3	Mutation(s): 0  Gene Names: PH0034
UniProt
Find proteins for O57746 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O57746  Go to UniProtKB:  O57746

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACY	D [auth A], E [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.216 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.169 (Depositor) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.751	α = 90
b = 82.751	β = 90
c = 84.814	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
CCP4	phasing
O	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-12-21 
Deposition Author(s): Cuff, M.E., Evdokimova, E., Mursleen, A., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2011-12-21
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary