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- PDB-6lh4: Crystal structural of MacroD1-ADPr complex -

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Basic information

Entry
Database: PDB / ID: 6lh4
TitleCrystal structural of MacroD1-ADPr complex
ComponentsADP-ribose glycohydrolase MACROD1
KeywordsHYDROLASE / MacroD1 / ADPR / catalysis / DNA repair
Function / homology
Function and homology information


O-acetyl-ADP-ribose deacetylase / peptidyl-glutamate ADP-deribosylation / ADP-ribosylglutamate hydrolase activity / protein de-ADP-ribosylation / purine nucleoside metabolic process / deacetylase activity / hydrolase activity, acting on glycosyl bonds / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / DNA damage response / nucleoplasm / nucleus
Similarity search - Function
Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like
Similarity search - Domain/homology
Chem-AR6 / ADP-ribose glycohydrolase MACROD1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.999 Å
AuthorsYang, X. / Ma, Y. / Li, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81672794 China
CitationJournal: DNA Repair (Amst) / Year: 2020
Title: Molecular basis for the MacroD1-mediated hydrolysis of ADP-ribosylation.
Authors: Yang, X. / Ma, Y. / Li, Y. / Dong, Y. / Yu, L.L. / Wang, H. / Guo, L. / Wu, C. / Yu, X. / Liu, X.
History
DepositionDec 6, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 15, 2023Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_validate_close_contact / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 29, 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 glycohydrolase MACROD1
B: ADP-ribose glycohydrolase MACROD1
C: ADP-ribose glycohydrolase MACROD1
D: ADP-ribose glycohydrolase MACROD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,6798
Polymers105,4424
Non-polymers2,2374
Water7,494416
1
A: ADP-ribose glycohydrolase MACROD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9202
Polymers26,3601
Non-polymers5591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ADP-ribose glycohydrolase MACROD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9202
Polymers26,3601
Non-polymers5591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: ADP-ribose glycohydrolase MACROD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9202
Polymers26,3601
Non-polymers5591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: ADP-ribose glycohydrolase MACROD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9202
Polymers26,3601
Non-polymers5591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.900, 106.200, 79.900
Angle α, β, γ (deg.)90.000, 120.000, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
ADP-ribose glycohydrolase MACROD1 / MACRO domain-containing protein 1 / O-acetyl-ADP-ribose deacetylase MACROD1 / Protein LRP16 / ...MACRO domain-containing protein 1 / O-acetyl-ADP-ribose deacetylase MACROD1 / Protein LRP16 / [Protein ADP-ribosylaspartate] hydrolase MACROD1 / [Protein ADP-ribosylglutamate] hydrolase MACROD1


Mass: 26360.488 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MACROD1, LRP16 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9BQ69, O-acetyl-ADP-ribose deacetylase, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#2: Chemical
ChemComp-AR6 / [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE / Adenosine-5-Diphosphoribose


Mass: 559.316 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H23N5O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / 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: 2.78 Å3/Da / Density % sol: 55.82 %
Crystal growTemperature: 291.1 K / Method: vapor diffusion, sitting drop / Details: 0.2M Sodium thiocyanate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.999→32.896 Å / Num. obs: 78021 / % possible obs: 89 % / Redundancy: 1.895 % / Biso Wilson estimate: 38.733 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rrim(I) all: 0.064 / Χ2: 0.979 / Net I/σ(I): 13.12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2-2.051.90.5731.681921011309101090.6440.8189.4
2.05-2.111.9010.4182.24186321121598030.7850.59187.4
2.11-2.171.8820.3112.83166581073988530.8660.4482.4
2.17-2.241.8880.3073.05165101044187460.8490.43483.8
2.24-2.311.9070.2743.58175171009791880.9040.38791
2.31-2.391.9070.214.2817399986591230.9320.29792.5
2.39-2.481.9120.1715.0616534942586480.9610.24191.8
2.48-2.581.9060.1366.315996924783930.9680.19390.8
2.58-2.71.9150.1097.6214636863076440.9780.15488.6
2.7-2.831.8450.07310.0512748839969110.9910.10382.3
2.83-2.981.9030.06511.4113988788073500.9930.09293.3
2.98-3.161.9210.04416.0513597757170790.9970.06293.5
3.16-3.381.9130.03420.5612396704064790.9980.04892
3.38-3.651.9130.02527.5911403659359620.9980.03690.4
3.65-41.8280.02231.89553605752260.9980.0386.3
4-4.471.8490.01638.998836546047800.9990.02387.5
4.47-5.161.9110.01542.528589480044940.9990.02193.6
5.16-6.321.8970.01540.717023405437020.9990.02291.3
6.32-8.941.8070.01346.124721314026120.9990.01983.2
8.94-32.8961.9410.0159.253171173016340.9990.01594.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.14_3260refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2X47

2x47


Resolution: 1.999→32.896 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2848 3688 4.86 %
Rwork0.2401 72160 -
obs0.2422 75848 97.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 151.64 Å2 / Biso mean: 47.8011 Å2 / Biso min: 18.51 Å2
Refinement stepCycle: final / Resolution: 1.999→32.896 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7404 0 144 416 7964
Biso mean--43.66 44.83 -
Num. residues----940
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.999-2.02510.28261280.2776268895
2.0251-2.05280.35411510.285278497
2.0528-2.08210.36381520.2968271997
2.0821-2.11320.33081070.2901282697
2.1132-2.14620.32931530.2753272997
2.1462-2.18140.3381350.2675264091
2.1814-2.2190.2981460.2753267595
2.219-2.25930.27941270.2617273496
2.2593-2.30280.27451190.2589281698
2.3028-2.34980.29881670.2389280498
2.3498-2.40090.29461310.2402274998
2.4009-2.45670.29491560.2542281698
2.4567-2.51810.34171600.2428278498
2.5181-2.58620.2037860.2444280498
2.5862-2.66220.32821370.2349288298
2.6622-2.74810.24391430.2346272397
2.7481-2.84630.27731580.229261292
2.8463-2.96020.31261620.2419284699
2.9602-3.09480.30511200.2326280899
3.0948-3.25780.2931740.2394278599
3.2578-3.46170.27931300.2307285799
3.4617-3.72870.2541780.2235277099
3.7287-4.10330.2721420.2273277897
4.1033-4.69560.27191350.2252286398
4.6956-5.91030.28461670.2355280699
5.9103-32.8960.26821240.242286296

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