6LFT | pdb_00006lft

Poa1p S30A mutant in complex with ADP-ribose

PDB DOI: https://doi.org/10.2210/pdb6LFT/pdb

Classification: HYDROLASE
Organism(s): Saccharomyces cerevisiae S288C
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2019-12-03 Released: 2020-12-09
Deposition Author(s): Chiu, Y.C., Hsu, C.H.
Funding Organization(s): Ministry of Science and Technology (Taiwan)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.57 Å
R-Value Free:
0.166 (Depositor), 0.166 (DCC)
R-Value Work:
0.151 (Depositor), 0.151 (DCC)
R-Value Observed:
0.152 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Expanding the Substrate Specificity of Macro Domains toward 3''-Isomer of O-Acetyl-ADP-ribose

Chiu, Y.C., Tseng, M.C., Hsu, C.H.

(2021) ACS Catal 11: 11075-11090

DOI: https://doi.org/10.1021/acscatal.1c01943

Macromolecule Content

Total Structure Weight: 20.85 kDa
Atom Count: 1,542
Modeled Residue Count: 166
Deposited Residue Count: 180
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-ribose 1''-phosphate phosphatase	A	180	Saccharomyces cerevisiae S288C	Mutation(s): 1 Gene Names: POA1, YBR022W, YBR0304 EC: 3.1.3.84 (PDB Primary Data), 3.2.2 (PDB Primary Data)
UniProt
Find proteins for P38218 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38218 Go to UniProtKB: P38218
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P38218
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
APR (Subject of Investigation/LOI) Query on APR Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ADENOSINE-5-DIPHOSPHORIBOSE C₁₅ H₂₃ N₅ O₁₄ P₂ SRNWOUGRCWSEMX-KEOHHSTQSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
ACT Query on ACT 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]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.57 Å
R-Value Free: 0.166 (Depositor), 0.166 (DCC)
R-Value Work: 0.151 (Depositor), 0.151 (DCC)
R-Value Observed: 0.152 (Depositor)

Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.218	α = 90
b = 82.218	β = 90
c = 52.416	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-12-09

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Science and Technology (Taiwan)	Taiwan	108-2628-B-002-013
Ministry of Science and Technology (Taiwan)	Taiwan	108-2113-M-002-011

Revision History (Full details and data files)

Version 1.0: 2020-12-09
Type: Initial release
Version 1.1: 2022-06-22
Changes: Database references
Version 1.2: 2023-11-22
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.