[English] 日本語
Yorodumi
- PDB-6lfs: Poa1p H23A mutant in complex with ADP-ribose -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6lfs
TitlePoa1p H23A mutant in complex with ADP-ribose
ComponentsADP-ribose 1''-phosphate phosphatase
KeywordsHYDROLASE / deacetylase / macro domain
Function / homology
Function and homology information


ADP-ribosyl-[dinitrogen reductase] hydrolase activity / tRNA splicing, via endonucleolytic cleavage and ligation / ADP-ribose 1''-phosphate phosphatase / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / phosphatase activity
Similarity search - Function
Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like
Similarity search - Domain/homology
ADENOSINE-5-DIPHOSPHORIBOSE / ADP-ribose 1''-phosphate phosphatase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsChiu, Y.C. / Hsu, C.H.
Funding support Taiwan, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (Taiwan)108-2628-B-002-013 Taiwan
Ministry of Science and Technology (Taiwan)108-2113-M-002-011 Taiwan
CitationJournal: Acs Catalysis / Year: 2021
Title: Expanding the Substrate Specificity of Macro Domains toward 3''-Isomer of O-Acetyl-ADP-ribose
Authors: Chiu, Y.C. / Tseng, M.C. / Hsu, C.H.
History
DepositionDec 3, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ADP-ribose 1''-phosphate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9583
Polymers20,1771
Non-polymers7812
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomeric protein
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-8 kcal/mol
Surface area7900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.429, 82.429, 52.588
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64

-
Components

#1: Protein ADP-ribose 1''-phosphate phosphatase / [Protein ADP-ribosylglutamate] hydrolase


Mass: 20177.020 Da / Num. of mol.: 1 / Mutation: H23A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: POA1, YBR022W, YBR0304 / Production host: Escherichia coli (E. coli)
References: UniProt: P38218, ADP-ribose 1''-phosphate phosphatase, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#2: Chemical ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N5O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID


Mass: 221.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.88 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop
Details: Sodium chloride, CAPS, Sodium hydroxide, PEG 8000, Glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.87→32.439 Å / Num. obs: 16602 / % possible obs: 99.8 % / Redundancy: 5.5 % / CC1/2: 0.981 / Net I/σ(I): 24.2
Reflection shellResolution: 1.87→1.93 Å / CC1/2: 0.937

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LFQ

6lfq


Resolution: 1.87→32.439 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 20.56
RfactorNum. reflection% reflection
Rfree0.2202 1658 9.99 %
Rwork0.1758 --
obs0.1802 16602 97.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 76.11 Å2 / Biso mean: 24.7408 Å2 / Biso min: 2.15 Å2
Refinement stepCycle: final / Resolution: 1.87→32.439 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1308 0 50 203 1561
Biso mean--15.85 33.71 -
Num. residues----166
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.87-1.92480.25261100.2115102282
1.9248-1.9870.26371340.193118093
1.987-2.0580.25551390.18651276100
2.058-2.14030.23721390.17981253100
2.1403-2.23770.24691390.1771267100
2.2377-2.35570.22781420.18481269100
2.3557-2.50320.23761420.18381279100
2.5032-2.69640.21261400.18531256100
2.6964-2.96760.21471350.1821281100
2.9676-3.39660.21621420.17841271100
3.3966-4.27780.2031470.15781276100
4.2778-32.4390.19711490.16391314100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.01540.03370.01630.06390.03720.02520.03060.14220.1029-0.08640.0162-0.1102-0.0793-0.00150.01350.1013-0.03250.02320.12470.04210.098710.7337-29.5969-6.5166
20.0091-0.00720.00510.0397-0.01370.0043-0.0259-0.02780.00420.0652-0.0141-0.04250.0171-0.07490.00060.07930.01190.03760.14260.01070.13151.5766-34.80766.7406
30.0037-0.0028-0.00110.0021-0.00010.0014-0.03930.0455-0.0769-0.03670.01550.00640.0362-0.0192-00.0975-0.00920.02410.09560.00560.09117.1189-41.50054.1271
40.01480.03720.00840.2220.05320.0160.0048-0.1491-0.05820.06670.046-0.0613-0.0595-0.1210.0165-0.03510.05910.02360.18510.03810.07581.4094-35.312516.8569
50.01330.01280.02980.01120.02690.05960.0263-0.1170.03750.02780.01080.0292-0.08630.05590.0390.02810.00660.02410.13950.00640.12416.546-30.56069.2733
60.14430.0912-0.05660.0807-0.00930.05010.02930.02520.041-0.02430.0090.0389-0.0073-0.04230.0825-0.0360.0141-0.02070.28130.08530.1152-12.2711-37.32835.9402
70.04710.0294-0.07050.0314-0.11380.48460.1473-0.06150.1562-0.02960.1171-0.0287-0.207-0.05110.1340.10820.11510.02880.14420.01770.2948-3.2158-21.54515.5563
80.0107-0.0055-0.00320.00950.00310.0024-0.0194-0.0123-0.0076-0.01050.0327-0.0347-0.05390.04840.00880.2308-0.03940.06310.3693-0.18560.238613.8641-25.273614.1867
90.0391-0.0623-0.06020.10030.08860.08770.04140.06840.1-0.14270.0175-0.0526-0.1465-0.06870.04010.1313-0.0171-0.01480.17490.06230.14462.7991-28.8907-0.6511
100.010.0071-0.02230.0059-0.01750.052-0.00480.05160.0667-0.0249-0.009-0.004-0.0564-0.0489-0.00920.30360.0942-0.02370.18990.13790.2334-4.5768-22.5313-5.7869
110.0492-0.0379-0.0120.06150.01790.01270.05130.09540.18070.03820.04790.0084-0.1239-0.06820.0220.19510.00890.04590.13560.10510.16145.1302-24.1525-5.2245
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 18 )A2 - 18
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 33 )A19 - 33
3X-RAY DIFFRACTION3chain 'A' and (resid 34 through 43 )A34 - 43
4X-RAY DIFFRACTION4chain 'A' and (resid 44 through 61 )A44 - 61
5X-RAY DIFFRACTION5chain 'A' and (resid 62 through 84 )A62 - 84
6X-RAY DIFFRACTION6chain 'A' and (resid 85 through 93 )A85 - 93
7X-RAY DIFFRACTION7chain 'A' and (resid 94 through 113 )A94 - 113
8X-RAY DIFFRACTION8chain 'A' and (resid 114 through 136 )A114 - 136
9X-RAY DIFFRACTION9chain 'A' and (resid 137 through 155 )A137 - 155
10X-RAY DIFFRACTION10chain 'A' and (resid 156 through 166 )A156 - 166
11X-RAY DIFFRACTION11chain 'A' and (resid 167 through 177 )A167 - 177

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more