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- PDB-6lft: Poa1p S30A mutant in complex with ADP-ribose -

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Basic information

Entry
Database: PDB / ID: 6lft
TitlePoa1p S30A 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
ACETATE ION / ADENOSINE-5-DIPHOSPHORIBOSE / ADP-ribose 1''-phosphate phosphatase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 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)20,8463
Polymers20,2281
Non-polymers6182
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomeric protein
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-8 kcal/mol
Surface area7810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.218, 82.218, 52.416
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: 20228.088 Da / Num. of mol.: 1 / Mutation: S30A
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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.53 Å3/Da / Density % sol: 51.35 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop
Details: Ammonium acetate, Sodium citrate tribasic dihydrate, PEG 4000, Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.57→24.595 Å / Num. obs: 27730 / % possible obs: 99 % / Redundancy: 5.2 % / CC1/2: 0.964 / Net I/σ(I): 28.7
Reflection shellResolution: 1.57→1.62 Å / CC1/2: 0.838

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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: 1.57→24.595 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.48
RfactorNum. reflection% reflection
Rfree0.1662 1987 7.17 %
Rwork0.1514 --
obs0.1525 27730 98.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 67.77 Å2 / Biso mean: 20.5567 Å2 / Biso min: 6.3 Å2
Refinement stepCycle: final / Resolution: 1.57→24.595 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1312 0 40 190 1542
Biso mean--13.45 33.61 -
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 (%)
1.5702-1.60950.20211210.1959154684
1.6095-1.6530.21971350.1771174493
1.653-1.70160.18651350.1677178597
1.7016-1.75650.17571410.16091859100
1.7565-1.81930.17751460.16341876100
1.8193-1.89210.16811420.1611864100
1.8921-1.97820.17151450.14541866100
1.9782-2.08240.14481470.14431883100
2.0824-2.21280.14761400.14721877100
2.2128-2.38350.17481510.15491861100
2.3835-2.62320.16911450.1571882100
2.6232-3.00220.18531370.16061867100
3.0022-3.78020.16571530.14421907100
3.7802-24.5950.14371490.13511926100
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)
13.1380.1184-0.52333.3673-0.37122.16170.0805-0.27910.13150.5878-0.0343-0.0955-0.02440.1702-0.03440.1358-0.0283-0.05830.1542-0.00630.0772-20.200124.06765.9471
22.07910.13360.26411.9878-0.31661.07280.038-0.0854-0.01930.00510.01640.1064-0.0093-0.1116-0.04440.0816-0.0153-0.00050.0684-0.00320.0701-30.480622.1128-6.106
32.20470.82350.76262.58622.53833.448-0.04630.25720.0019-0.58160.00310.152-0.00680.0829-0.01440.1483-0.0346-0.02520.1162-0.00530.0906-29.91718.7275-17.4231
42.28472.247-0.06196.2848-0.43921.16440.01170.0411-0.1407-0.20140.017-0.24450.0240.132-0.03960.0824-0.0228-0.01210.0778-0.01370.0903-23.086520.8307-9.8672
54.388-1.179-1.26174.357-1.79117.33720.1941-0.2759-0.49630.30040.10740.13180.3394-0.5063-0.18860.1516-0.0959-0.04760.1040.02420.1844-38.48258.089-6.46
64.5382.407-2.28384.3577-0.56784.5960.1561-0.3267-0.6925-0.1031-0.0476-0.51280.50070.58010.06950.19370.046-0.08210.0827-0.00270.2668-20.27047.8904-6.1901
73.39532.56531.89492.57430.84272.4239-0.24050.81810.0151-0.30270.3094-0.1076-0.3840.5843-0.12590.2474-0.08260.08130.3437-0.07060.1826-14.977824.5105-14.8587
82.49450.9565-0.34082.429-0.06241.97650.0848-0.4389-0.22370.1296-0.0124-0.13490.20030.1445-0.02040.1134-0.0166-0.03590.0850.02890.1008-23.492216.78650.1025
92.38921.778-2.30892.5952-1.85094.63750.1247-0.4719-0.63090.46820.0547-0.49080.56030.2660.08080.3180.0191-0.12690.20360.07640.2608-21.587.20534.9349
108.7394-4.2752-1.28416.66320.48073.86580.023-0.3958-0.37130.32020.082-0.27980.3020.4276-0.00090.1520.0033-0.0880.16550.03160.154-18.288416.40944.5651
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 43 )A19 - 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 93 )A85 - 93
6X-RAY DIFFRACTION6chain 'A' and (resid 94 through 113 )A94 - 113
7X-RAY DIFFRACTION7chain 'A' and (resid 114 through 136 )A114 - 136
8X-RAY DIFFRACTION8chain 'A' and (resid 137 through 155 )A137 - 155
9X-RAY DIFFRACTION9chain 'A' and (resid 156 through 166 )A156 - 166
10X-RAY DIFFRACTION10chain 'A' and (resid 167 through 177 )A167 - 177

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