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- PDB-6lfq: Crystal structure of Poa1p in apo form -

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Basic information

Entry
Database: PDB / ID: 6lfq
TitleCrystal structure of Poa1p in apo form
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
ADP-ribose 1''-phosphate phosphatase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.359 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 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)20,3362
Polymers20,2441
Non-polymers921
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomeric protein
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-1 kcal/mol
Surface area8270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.195, 59.612, 100.658
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-310-

HOH

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Components

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


Mass: 20244.090 Da / Num. of mol.: 1
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 1.82 Å3/Da / Density % sol: 32.52 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop
Details: HEPES sodium, Lithium sulfate monohydrate, Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / 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: 2.359→29.806 Å / Num. obs: 6209 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 0.971 / Net I/σ(I): 14
Reflection shellResolution: 2.359→2.444 Å / CC1/2: 0.911

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.359→29.806 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.19
RfactorNum. reflection% reflection
Rfree0.2552 621 10 %
Rwork0.1601 --
obs0.1694 6209 97.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 88.16 Å2 / Biso mean: 29.5345 Å2 / Biso min: 8.36 Å2
Refinement stepCycle: final / Resolution: 2.359→29.806 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1336 0 6 52 1394
Biso mean--42.8 31.78 -
Num. residues----169
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.359-2.59610.32091400.2008126790
2.5961-2.97150.27111560.19331398100
2.9715-3.74260.2771580.1571142899
3.7426-29.8060.21571670.13841495100
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)
10.6516-0.4383-0.4520.1288-0.05610.4666-0.08480.063-0.20760.05490.0551-0.04880.001-0.09380.00610.13150.0053-0.00610.14980.01510.10949.578711.161916.3263
20.1445-0.01410.00020.3281-0.03890.0379-0.28020.42440.1584-0.34970.27250.48620.16970.2722-0.04310.11580.0083-0.0790.0774-0.03670.15813.13899.872511.9194
30.2535-0.06560.05730.0403-0.05840.0988-0.03890.03830.03830.0405-0.0375-0.235-0.11090.0543-0.02260.122-0.0103-0.00640.12010.0180.147820.297319.526116.3802
40.02620.03270.02060.097-0.06760.07730.00260.3444-0.38750.0006-0.4850.14970.11330.2895-0.00920.34150.007-0.06520.2038-0.03120.111314.90666.95342.5289
50.4977-0.0052-0.17870.21820.02940.33730.14830.06970.1918-0.0949-0.0523-0.2026-0.46290.03970.00960.13060.05620.03970.11170.03210.153510.659524.506613.7312
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 61 )A2 - 61
2X-RAY DIFFRACTION2chain 'A' and (resid 62 through 84 )A62 - 84
3X-RAY DIFFRACTION3chain 'A' and (resid 85 through 115 )A85 - 115
4X-RAY DIFFRACTION4chain 'A' and (resid 116 through 136 )A116 - 136
5X-RAY DIFFRACTION5chain 'A' and (resid 137 through 177 )A137 - 177

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