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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.173 (Depositor), 0.171 (DCC)
R-Value Work:
0.139 (Depositor), 0.140 (DCC)
R-Value Observed:
0.139 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 7EJ3

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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

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

Find similar proteins by:

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	3D Interactions
DPO (Subject of Investigation/LOI) Query on DPO Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B]	D [auth A], G [auth B]	DIPHOSPHATE O₇ P₂ XPPKVPWEQAFLFU-UHFFFAOYSA-J		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
GLY Query on GLY Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	GLYCINE C₂ H₅ N O₂ DHMQDGOQFOQNFH-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain C [auth A]	C [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.173 (Depositor), 0.171 (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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-09-21

Deposition Author(s):

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.