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- PDB-6y73: The crystal structure of human MACROD2 in space group P43 -

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Basic information

Entry
Database: PDB / ID: 6y73
TitleThe crystal structure of human MACROD2 in space group P43
ComponentsADP-ribose glycohydrolase MACROD2
KeywordsHYDROLASE / ADP-ribosylhydrolase / macrodomain
Function / homology
Function and homology information


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; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / response to bacterium / brain development ...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; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / response to bacterium / brain development / DNA damage response / nucleolus / nucleoplasm / nucleus
Similarity search - Function
Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like
Similarity search - Domain/homology
L(+)-TARTARIC ACID / ADP-ribose glycohydrolase MACROD2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsWazir, S. / Maksimainen, M.M. / Lehtio, L.
Funding support Finland, 2items
OrganizationGrant numberCountry
Academy of Finland287063 Finland
Academy of Finland294085 Finland
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: Multiple crystal forms of human MacroD2.
Authors: Wazir, S. / Maksimainen, M.M. / Lehtio, L.
History
DepositionFeb 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ADP-ribose glycohydrolase MACROD2
B: ADP-ribose glycohydrolase MACROD2
C: ADP-ribose glycohydrolase MACROD2
D: ADP-ribose glycohydrolase MACROD2
E: ADP-ribose glycohydrolase MACROD2
F: ADP-ribose glycohydrolase MACROD2
G: ADP-ribose glycohydrolase MACROD2
H: ADP-ribose glycohydrolase MACROD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)328,62220
Polymers327,2558
Non-polymers1,36712
Water28,6981593
1
A: ADP-ribose glycohydrolase MACROD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9992
Polymers40,9071
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ADP-ribose glycohydrolase MACROD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1493
Polymers40,9071
Non-polymers2422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: ADP-ribose glycohydrolase MACROD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3195
Polymers40,9071
Non-polymers4124
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: ADP-ribose glycohydrolase MACROD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9992
Polymers40,9071
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: ADP-ribose glycohydrolase MACROD2


Theoretical massNumber of molelcules
Total (without water)40,9071
Polymers40,9071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: ADP-ribose glycohydrolase MACROD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1353
Polymers40,9071
Non-polymers2282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: ADP-ribose glycohydrolase MACROD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0572
Polymers40,9071
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: ADP-ribose glycohydrolase MACROD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0572
Polymers40,9071
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.780, 96.780, 261.090
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: Protein
ADP-ribose glycohydrolase MACROD2 / MACRO domain-containing protein 2 / O-acetyl-ADP-ribose deacetylase MACROD2 / [Protein ADP- ...MACRO domain-containing protein 2 / O-acetyl-ADP-ribose deacetylase MACROD2 / [Protein ADP-ribosylaspartate] hydrolase MACROD2 / [Protein ADP-ribosylglutamate] hydrolase MACROD2


Mass: 40906.844 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MACROD2, C20orf133 / Production host: Escherichia coli (E. coli)
References: UniProt: A1Z1Q3, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1593 / 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: 1.87 Å3/Da / Density % sol: 34.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 0.2 M Ammonium tartarate dibasic pH 6.7, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91589 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91589 Å / Relative weight: 1
ReflectionResolution: 1.7→48.39 Å / Num. obs: 261897 / % possible obs: 100 % / Redundancy: 6.963 % / Biso Wilson estimate: 30.535 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.123 / Rrim(I) all: 0.133 / Χ2: 0.974 / Net I/σ(I): 8.98 / Num. measured all: 1823516 / Scaling rejects: 23
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
1.7-1.747.0631.151.4113669119354193540.611.242100
1.74-1.796.9710.9331.7813184318912189120.7121.008100
1.79-1.846.8550.7182.3712557418320183190.8050.777100
1.84-1.96.5150.5742.8911657417893178930.8750.624100
1.9-1.966.6970.433.9711524517209172080.9180.466100
1.96-2.037.1760.3385.1911989916709167080.9530.364100
2.03-2.117.1450.2646.5411522116127161270.9690.285100
2.11-2.197.1110.2147.9711020615497154970.9770.231100
2.19-2.297.0570.189.3110501814882148820.9780.195100
2.29-2.46.6880.1679.729534814257142570.9840.181100
2.4-2.536.6850.14311.219045513532135320.9860.156100
2.53-2.697.2840.13312.849335812816128160.9880.143100
2.69-2.877.2770.11814.428722611987119870.990.127100
2.87-3.17.1720.10316.318040111210112100.9910.111100
3.1-3.46.8540.09118.027061910304103040.9920.099100
3.4-3.86.5590.08419.2561308934793470.9930.091100
3.8-4.397.3670.08321.2660656823482340.9940.09100
4.39-5.387.1930.08321.250129696969690.9930.089100
5.38-7.66.6090.08119.9435475536853680.9930.088100
7.6-48.397.4910.0823.0222270298529730.9950.08599.6

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IQY

4iqy


Resolution: 1.7→48.39 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.093 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.088
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2031 13095 5 %RANDOM
Rwork0.1821 ---
obs0.1831 248801 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 90.27 Å2 / Biso mean: 25.568 Å2 / Biso min: 13.31 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å2-0 Å2-0 Å2
2--0.45 Å2-0 Å2
3----0.9 Å2
Refinement stepCycle: final / Resolution: 1.7→48.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13673 0 88 1603 15364
Biso mean--37.11 32.29 -
Num. residues----1729
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01314285
X-RAY DIFFRACTIONr_bond_other_d0.0010.01713694
X-RAY DIFFRACTIONr_angle_refined_deg1.3521.64119287
X-RAY DIFFRACTIONr_angle_other_deg1.3251.58231823
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.52951794
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.26821.884722
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.028152660
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4141596
X-RAY DIFFRACTIONr_chiral_restr0.0710.21858
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215776
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022980
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 966 -
Rwork0.327 18357 -
all-19323 -
obs--99.99 %

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