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- PDB-6lfs: Poa1p H23A mutant in complex with ADP-ribose -

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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 / 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: 1.87 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

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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)20,9583
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

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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

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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: 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

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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 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

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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

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