7DRZ | pdb_00007drz

Crystal structure of Aspergillus oryzae Rib2 deaminase (C-terminal deletion mutant) at pH 4.6

PDB DOI: https://doi.org/10.2210/pdb7DRZ/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Aspergillus oryzae RIB40
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-12-30 Released: 2021-07-14
Deposition Author(s): Chen, S.C., Liaw, S.H., Hsu, C.H.
Funding Organization(s): Ministry of Science and Technology (MoST, Taiwan)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.211 (Depositor), 0.212 (DCC)
R-Value Work:
0.195 (Depositor), 0.195 (DCC)
R-Value Observed:
0.196 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 7DRZ

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

Literature

Crystal structures of Aspergillus oryzae Rib2 deaminase: the functional mechanism involved in riboflavin biosynthesis.

Chen, S.C., Ye, L.C., Yen, T.M., Zhu, R.X., Li, C.Y., Chang, S.C., Liaw, S.H., Hsu, C.H.

(2021) IUCrJ 8: 549-558

DOI: https://doi.org/10.1107/S205225252100275X

Macromolecule Content

Total Structure Weight: 22.09 kDa
Atom Count: 1,575
Modeled Residue Count: 186
Deposited Residue Count: 196
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CMP/dCMP-type deaminase domain-containing protein	A	196	Aspergillus oryzae RIB40	Mutation(s): 0 Gene Names: AO090026000280
UniProt
Find proteins for Q2UFA9 (Aspergillus oryzae (strain ATCC 42149 / RIB 40)) Explore Q2UFA9 Go to UniProtKB: Q2UFA9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2UFA9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.211 (Depositor), 0.212 (DCC)
R-Value Work: 0.195 (Depositor), 0.195 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.093	α = 90
b = 87.093	β = 90
c = 61.215	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-07-14

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, Taiwan)	Taiwan	--

Revision History (Full details and data files)

Version 1.0: 2021-07-14
Type: Initial release
Version 1.1: 2024-03-27
Changes: Data collection, Database references

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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.