7DS1

Crystal structure of Aspergillus oryzae Rib2 deaminase in complex with DARIPP (C-terminal deletion mutant at pH 6.5)

PDB DOI: https://doi.org/10.2210/pdb7DS1/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: 1.58 Å
R-Value Free: 0.208
R-Value Work: 0.183
R-Value Observed: 0.184

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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: 22.44 kDa
Atom Count: 1,654
Modelled Residue Count: 183
Deposited Residue Count: 196
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2UFA9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HJL (Subject of Investigation/LOI) Query on HJL Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	[(2~{R},3~{S},4~{S})-5-[[2,5-bis(azanyl)-6-oxidanylidene-1~{H}-pyrimidin-4-yl]amino]-2,3,4-tris(oxidanyl)pentyl] dihydrogen phosphate C₉ H₁₈ N₅ O₈ P ACIVVGBVOVHFPQ-RPDRRWSUSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 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: 1.58 Å
R-Value Free: 0.208
R-Value Work: 0.183
R-Value Observed: 0.184
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.32	α = 90
b = 90.778	β = 90
c = 40.833	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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Ligand Structure Quality Assessment

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.