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- PDB-6y4z: The crystal structure of human MACROD2 in space group P43212 -

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Basic information

Entry
Database: PDB / ID: 6y4z
TitleThe crystal structure of human MACROD2 in space group P43212
ComponentsThioredoxin 1,ADP-ribose glycohydrolase MACROD2
KeywordsHYDROLASE / ADP-ribosylhydrolase / macrodomain
Function / homology
Function and homology information


ADP-ribosylglutamate hydrolase activity / protein de-ADP-ribosylation / peptidyl-glutamate ADP-deribosylation / 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 / DNA polymerase processivity factor activity / protein-disulfide reductase activity ...ADP-ribosylglutamate hydrolase activity / protein de-ADP-ribosylation / peptidyl-glutamate ADP-deribosylation / 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 / DNA polymerase processivity factor activity / protein-disulfide reductase activity / cell redox homeostasis / response to bacterium / brain development / DNA damage response / nucleolus / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. ...Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Thioredoxin-like superfamily / Macro domain-like
Similarity search - Domain/homology
L(+)-TARTARIC ACID / ADP-ribose glycohydrolase MACROD2 / Thioredoxin 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 24, 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: Thioredoxin 1,ADP-ribose glycohydrolase MACROD2
B: Thioredoxin 1,ADP-ribose glycohydrolase MACROD2
C: Thioredoxin 1,ADP-ribose glycohydrolase MACROD2
D: Thioredoxin 1,ADP-ribose glycohydrolase MACROD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,7775
Polymers163,6274
Non-polymers1501
Water7,909439
1
A: Thioredoxin 1,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
2
B: Thioredoxin 1,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
3
C: Thioredoxin 1,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
4
D: Thioredoxin 1,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)95.360, 95.360, 261.920
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
Thioredoxin 1,ADP-ribose glycohydrolase MACROD2 / Trx-1 / MACRO domain-containing protein 2 / O-acetyl-ADP-ribose deacetylase MACROD2 / [Protein ADP- ...Trx-1 / 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.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Homo sapiens (human)
Gene: trxA, fipA, tsnC, b3781, JW5856, MACROD2, C20orf133 / Production host: Escherichia coli (E. coli)
References: UniProt: P0AA25, UniProt: A1Z1Q3, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 439 / 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

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: 0.9762 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.9→47.73 Å / Num. obs: 95967 / % possible obs: 100 % / Redundancy: 13.348 % / Biso Wilson estimate: 42.232 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.081 / Rrim(I) all: 0.085 / Χ2: 1.046 / Net I/σ(I): 18.92 / Num. measured all: 1280920 / 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
1.9-1.9511.3951.651.2579871701170090.7461.729100
1.95-212.9551.2571.987862678367820.8671.309100
2-2.0614.0740.9372.8193549664766470.9320.972100
2.06-2.1213.9620.7073.7290016644764470.9550.734100
2.12-2.1913.8790.5394.8586719625162480.9750.56100
2.19-2.2713.6360.416.2582868607760770.9860.426100
2.27-2.3613.0390.3257.575955582858250.9890.33899.9
2.36-2.4513.6780.289.1277690568156800.990.291100
2.45-2.5613.2310.21611.4671474540254020.9940.224100
2.56-2.6914.0190.18413.8772635518151810.9950.191100
2.69-2.8313.990.14117.9269391496049600.9970.146100
2.83-313.7610.10823.0164897471647160.9980.113100
3-3.2113.3480.07831.2959133443044300.9990.081100
3.21-3.4712.8580.05839.7853000412241220.9990.061100
3.47-3.812.9650.04848.3949798384138410.9990.05100
3.8-4.2513.8420.04156.57481153476347610.042100
4.25-4.9113.6780.03761.54424143101310110.038100
4.91-6.0112.880.03758.5134312266426640.9990.038100
6.01-8.512.3640.03260.63261492115211510.033100
8.5-47.7312.1160.02477.1415072125612440.9990.02599

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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: 1.9→47.73 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.958 / SU B: 4.095 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.125
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2277 4765 5 %RANDOM
Rwork0.2005 ---
obs0.2018 91202 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 117.45 Å2 / Biso mean: 42.981 Å2 / Biso min: 14.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.68 Å2-0 Å2-0 Å2
2--1.68 Å2-0 Å2
3----3.37 Å2
Refinement stepCycle: final / Resolution: 1.9→47.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6856 0 10 440 7306
Biso mean--42.53 43.21 -
Num. residues----866
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0137074
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176793
X-RAY DIFFRACTIONr_angle_refined_deg1.5631.6389541
X-RAY DIFFRACTIONr_angle_other_deg1.3671.58215766
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7445878
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.44421.816358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.958151317
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3531548
X-RAY DIFFRACTIONr_chiral_restr0.0780.2917
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027811
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021481
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 339 -
Rwork0.353 6660 -
all-6999 -
obs--99.81 %

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