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- PDB-6lfr: Poa1p in complex with ADP-ribose -

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Basic information

Entry
Database: PDB / ID: 6lfr
TitlePoa1p 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 / purine nucleoside metabolic process / tRNA splicing, via endonucleolytic cleavage and ligation / ADP-ribose 1''-phosphate phosphatase / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / phosphatase activity / DNA damage response / nucleoplasm
Similarity search - Function
: / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain / 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: 1.78 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)20,8032
Polymers20,2441
Non-polymers5591
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomeric protein
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-7 kcal/mol
Surface area7860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.619, 85.619, 37.945
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64
Components on special symmetry positions
IDModelComponents
11A-425-

HOH

21A-437-

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-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N5O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.98 Å3/Da / Density % sol: 37.98 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop
Details: Ammonium sulfate, Sodium cacodylate trihydrate, PEG 8000, Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Mar 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.02
ReflectionResolution: 1.78→26.518 Å / Num. obs: 15302 / % possible obs: 99.2 % / Redundancy: 9.7 % / CC1/2: 0.985 / Net I/σ(I): 51.3
Reflection shellResolution: 1.78→1.84 Å / CC1/2: 0.917

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LFQ

6lfq


Resolution: 1.78→26.518 Å / Cross valid method: THROUGHOUT / σ(F): 3.14 / Phase error: 20.43
RfactorNum. reflection% reflection
Rfree0.2029 1521 10.08 %
Rwork0.1751 --
obs0.1781 15094 97.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 95.33 Å2 / Biso mean: 28.9327 Å2 / Biso min: 8.25 Å2
Refinement stepCycle: final / Resolution: 1.78→26.518 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1313 0 36 177 1526
Biso mean--20.62 46.51 -
Num. residues----166
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7812-1.83870.30271190.21791063118277
1.8387-1.90430.2311390.21391263140290
1.9043-1.98050.22111380.20961232137090
1.9805-2.07050.24441390.20681226136590
2.0705-2.17950.26211360.19841269140590
2.1795-2.31580.20441450.20481249139490
2.3158-2.49420.2271370.19011248138590
2.4942-2.74450.20951460.20411268141490
2.7445-3.13990.19591390.17781255139490
3.1399-3.94950.19531370.13731275141290
3.9495-18.38130.15991360.14091218135484
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)
10.9216-0.39060.13282.0252-0.16891.61440.21470.62160.1198-0.2352-0.26020.14320.13720.15370.02540.11080.0361-0.01690.21640.00370.1424.685722.9143-2.9557
24.91560.6133-4.08743.90843.66047.93780.13480.30750.6467-0.3447-0.0224-0.1027-0.38850.1663-0.08890.1312-0.02430.00540.20430.09940.206333.319427.59140.2561
32.0104-0.0755-0.31854.3778-2.20242.4229-0.1273-0.40290.0930.3668-0.0532-0.0153-0.06520.07880.11420.14570.044-0.04270.1305-0.01440.143932.836718.64612.8606
43.2098-2.3342-0.336.78720.97332.7657-0.0631-0.08770.00490.22560.07150.2029-0.0133-0.1019-0.00210.09020.0151-0.01910.1009-0.01550.131425.069221.39296.7116
51.4556-0.429-0.13411.8081-0.02231.37420.16540.3582-0.5265-0.0584-0.03070.48150.4075-0.04620.08870.25620.0386-0.08510.1896-0.10990.435525.97898.83891.8825
64.4502-2.18561.37992.09470.11342.2536-0.1749-0.6539-0.10080.33470.1454-0.05750.1164-0.0520.0220.21720.0280.03130.3034-0.01620.171217.988724.879913.1199
70.6967-0.1845-0.83530.92440.17391.55290.14690.3636-0.1989-0.1197-0.0380.01730.16950.03590.20440.16070.0725-0.04840.2721-0.11560.136523.558918.2094-3.4942
80.3752-0.2343-0.63070.5730.9762.2903-0.02960.1588-0.14880.07140.00590.00660.4923-0.12010.18910.36740.059-0.13870.4222-0.26610.47520.2499.0321-8.3467
96.84273.8445-1.61665.5715-2.31533.1686-0.190.5526-0.2546-0.32550.0490.3850.1877-0.40580.0210.21810.0606-0.09030.3879-0.1270.260817.598318.3264-6.8658
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 33 )A2 - 33
2X-RAY DIFFRACTION2chain 'A' and (resid 34 through 43 )A34 - 43
3X-RAY DIFFRACTION3chain 'A' and (resid 44 through 61 )A44 - 61
4X-RAY DIFFRACTION4chain 'A' and (resid 62 through 84 )A62 - 84
5X-RAY DIFFRACTION5chain 'A' and (resid 85 through 113 )A85 - 113
6X-RAY DIFFRACTION6chain 'A' and (resid 114 through 136 )A114 - 136
7X-RAY DIFFRACTION7chain 'A' and (resid 137 through 155 )A137 - 155
8X-RAY DIFFRACTION8chain 'A' and (resid 156 through 166 )A156 - 166
9X-RAY DIFFRACTION9chain 'A' and (resid 167 through 177 )A167 - 177

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