5ZER | pdb_00005zer

UDP Glucose alpha tetrahydrobiopterin glycosyltransferase from Synechococcus species PCC 7942 - BH2 complex form

• PDB DOI: https://doi.org/10.2210/pdb5ZER/pdb

• Classification: TRANSFERASE
• Organism(s): Synechococcus elongatus PCC 7942 = FACHB-805
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-02-27 Released: 2019-03-06 
• Deposition Author(s): Killivalavan, A., Lee, K.H.
• Funding Organization(s): National Research Foundation (Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 
  0.286 (Depositor), 0.283 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Model: experimental

Literature

UDP Glucose alpha tetrahydrobiopterin glycosyltransferase from Synechococcus species PCC 7942 - BH2 complex form

Killivalavan, A., Lee, K.H.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 77.38 kDa 
• Atom Count: 5,525 
• Modeled Residue Count: 700 
• Deposited Residue Count: 708 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-glucose:tetrahydrobiopterin glucosyltransferase	A, B	354	Synechococcus elongatus PCC 7942 = FACHB-805	Mutation(s): 0
UniProt
Find proteins for Q31LX1 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805)) Explore Q31LX1  Go to UniProtKB:  Q31LX1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HBI (Subject of Investigation/LOI)	C [auth A], E [auth B]	7,8-DIHYDROBIOPTERIN C9 H13 N5 O3 FEMXZDUTFRTWPE-DZSWIPIPSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-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: 2.39 Å
• R-Value Free:  0.286 (Depositor), 0.283 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 167.13	α = 90
b = 80	β = 91.27
c = 53.38	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-03-06 
Deposition Author(s): Killivalavan, A., Lee, K.H.

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Funding Organization	Location	Grant Number
National Research Foundation (Korea)	Korea, Republic Of	NRF-2012R1A1A2044394

Revision History  

• Version 1.0: 2019-03-06
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary