7EJ3 | pdb_00007ej3

UTP cyclohydrolase

• PDB DOI: https://doi.org/10.2210/pdb7EJ3/pdb

• Classification: HYDROLASE
• Organism(s): Rhodococcus wratislaviensis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-04-01 Released: 2022-09-21 
• Deposition Author(s): Zhang, H., Zhang, Y., Yuchi, Z.
• Funding Organization(s): National Science Foundation (NSF, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.173 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.139 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.139 (Depositor) 

Literature

Structural and biochemical investigation of UTP cyclohydrolase

Zhang, H., Wei, Y., Lin, L., Liu, J., Chu, R., Cao, P., Ang, E.L., Zhao, H., Yuchi, Z., Zhang, Y.

(2021) ACS Catal : 8895-8901

• DOI: https://doi.org/10.1021/acscatal.1c02252

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: 91.44 kDa 
• Atom Count: 7,216 
• Modeled Residue Count: 798 
• Deposited Residue Count: 846 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTP cyclohydrolase II	A, B	423	Rhodococcus wratislaviensis	Mutation(s): 0  Gene Names: C8E05_0284

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DPO (Subject of Investigation/LOI)	D [auth A], G [auth B]	DIPHOSPHATE O7 P2 XPPKVPWEQAFLFU-UHFFFAOYSA-J
GLY	E [auth B]	GLYCINE C2 H5 N O2 DHMQDGOQFOQNFH-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)	C [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.173 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.139 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.139 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.152	α = 90
b = 115.152	β = 90
c = 283.489	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
AutoSol	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-09-21 
Deposition Author(s): Zhang, H., Zhang, Y., Yuchi, Z.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	31870049

Revision History  

• Version 1.0: 2022-09-21
  Type: Initial release
  
• Version 1.1: 2024-05-29
  Changes: Data collection, Refinement description