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- PDB-6y4y: The crystal structure of human MACROD2 in space group P41212 -

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Basic information

Entry
Database: PDB / ID: 6y4y
TitleThe crystal structure of human MACROD2 in space group P41212
ComponentsThioredoxin 1,ADP-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 / DNA polymerase processivity factor activity / protein-disulfide reductase activity ...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 / 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. / Macro domain-like / Thioredoxin-like superfamily
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 / molecular replacement / Resolution: 1.75 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
Water9,206511
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0572
Polymers40,9071
Non-polymers1501
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


Theoretical massNumber of molelcules
Total (without water)40,9071
Polymers40,9071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.650, 95.650, 258.720
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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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


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


Mass: 18.015 Da / Num. of mol.: 511 / 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: ESRF / Beamline: ID23-1 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.75→47.83 Å / Num. obs: 121564 / % possible obs: 100 % / Redundancy: 12.116 % / Biso Wilson estimate: 37.437 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.107 / Rrim(I) all: 0.112 / Χ2: 1.001 / Net I/σ(I): 13.27 / Num. measured all: 1472885 / Scaling rejects: 22
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
1.75-1.811.751.5421.7104148886288640.7091.613100
1.8-1.8411.7851.2252.2102140866986670.811.281100
1.84-1.911.780.9782.7898513836483630.8721.023100
1.9-1.9611.1560.7193.7191482820182000.920.754100
1.96-2.0212.0590.555.0795580792779260.9550.575100
2.02-2.0912.4640.4046.8695883769476930.9760.422100
2.09-2.1712.4170.338.4791986740974080.9840.345100
2.17-2.2612.2880.26410.1888004716271620.9890.275100
2.26-2.3611.7370.22711.3980525686168610.9910.237100
2.36-2.4712.7120.18813.9283594657665760.9940.196100
2.47-2.6113.3460.15416.8383984629362930.9950.16100
2.61-2.7713.3540.13318.9179281593759370.9960.139100
2.77-2.9612.8370.10522.271966560656060.9970.109100
2.96-3.2120.08325.4763122526052600.9980.087100
3.2-3.512.7910.07429.8661780483048300.9980.077100
3.5-3.9112.0880.07131.3153248440544050.9980.074100
3.91-4.5210.7950.07131.242445393539320.9970.07599.9
4.52-5.5311.5620.0732.5638733335133500.9980.073100
5.53-7.8311.3270.0732.230119265926590.9970.073100
7.83-47.8310.4020.06832.2616352158215720.9980.07299.4

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Phasing

PhasingMethod: molecular replacement

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Processing

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

4iqy


Resolution: 1.75→47.83 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.712 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.102
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2274 6079 5 %RANDOM
Rwork0.2043 ---
obs0.2055 115484 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 102.18 Å2 / Biso mean: 33.887 Å2 / Biso min: 17.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å2-0 Å2-0 Å2
2--1.01 Å2-0 Å2
3----2.02 Å2
Refinement stepCycle: final / Resolution: 1.75→47.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6830 0 10 511 7351
Biso mean--30.42 36.12 -
Num. residues----864
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0137029
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176728
X-RAY DIFFRACTIONr_angle_refined_deg1.4391.6379482
X-RAY DIFFRACTIONr_angle_other_deg1.3431.58215612
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8055870
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.121.977354
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.309151296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1851546
X-RAY DIFFRACTIONr_chiral_restr0.0750.2912
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027769
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021465
LS refinement shellResolution: 1.75→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 443 -
Rwork0.309 8413 -
all-8856 -
obs--100 %

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