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- PDB-7ny7: Crystal structure of the Capsaspora owczarzaki macroH2A macrodoma... -

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Basic information

Entry
Database: PDB / ID: 7ny7
TitleCrystal structure of the Capsaspora owczarzaki macroH2A macrodomain in complex with ADP-ribose
ComponentsHistone macroH2A1.1
KeywordsNUCLEAR PROTEIN / macrodomain / ADP-ribose / NAD+ metabolism / PARP1
Function / homology
Function and homology information


regulation of NAD metabolic process / ADP-D-ribose binding / ADP-D-ribose modification-dependent protein binding / negative regulation of protein ADP-ribosylation / structural constituent of chromatin / nucleosome / chromatin organization / protein heterodimerization activity / DNA binding / nucleus
Similarity search - Function
Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Macro domain ...Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like
Similarity search - Domain/homology
ADENOSINE-5-DIPHOSPHORIBOSE / Histone macroH2A1.1
Similarity search - Component
Biological speciesCapsaspora owczarzaki
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGuberovic, I. / Knobloch, G. / Basquin, J. / Buschbeck, M. / Ladurner, A.G.
Funding support Spain, European Union, 2items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesRTI2018-094005-B-I00 Spain
European CommissionH2020-MSCA-ITN-2015-675610European Union
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2021
Title: Evolution of a histone variant involved in compartmental regulation of NAD metabolism.
Authors: Guberovic, I. / Hurtado-Bages, S. / Rivera-Casas, C. / Knobloch, G. / Malinverni, R. / Valero, V. / Leger, M.M. / Garcia, J. / Basquin, J. / Gomez de Cedron, M. / Frigole-Vivas, M. / Cheema, ...Authors: Guberovic, I. / Hurtado-Bages, S. / Rivera-Casas, C. / Knobloch, G. / Malinverni, R. / Valero, V. / Leger, M.M. / Garcia, J. / Basquin, J. / Gomez de Cedron, M. / Frigole-Vivas, M. / Cheema, M.S. / Perez, A. / Ausio, J. / Ramirez de Molina, A. / Salvatella, X. / Ruiz-Trillo, I. / Eirin-Lopez, J.M. / Ladurner, A.G. / Buschbeck, M.
History
DepositionMar 21, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 2, 2022Group: Database references / Category: citation / citation_author
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.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: 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: Histone macroH2A1.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7525
Polymers23,0071
Non-polymers7464
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-4 kcal/mol
Surface area8140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.392, 71.392, 81.260
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Histone macroH2A1.1


Mass: 23006.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Capsaspora owczarzaki (strain ATCC 30864) (eukaryote)
Strain: ATCC 30864 / Gene: CAOG_004778 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D2UG83
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#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.: 176 / 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: 2.6 Å3/Da / Density % sol: 52.66 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.2M ammonium tartarate dibasic 20% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: May 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34 Å / Relative weight: 1
ReflectionResolution: 2→17.85 Å / Num. obs: 16593 / % possible obs: 96.14 % / Redundancy: 4.5 % / Biso Wilson estimate: 16.96 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.04 / Rrim(I) all: 0.051 / Net I/σ(I): 20.2
Reflection shellResolution: 2→2.071 Å / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1608 / CC1/2: 0.7 / Rrim(I) all: 0.84

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Processing

Software
NameVersionClassification
PHENIX(dev_3126: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IID

3iid


Resolution: 2→17.848 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 18.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2054 1610 10.07 %
Rwork0.1583 --
obs0.163 15983 96.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→17.848 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1324 0 48 176 1548
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051399
X-RAY DIFFRACTIONf_angle_d0.9481903
X-RAY DIFFRACTIONf_dihedral_angle_d12.82801
X-RAY DIFFRACTIONf_chiral_restr0.051226
X-RAY DIFFRACTIONf_plane_restr0.004235
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.06460.32251340.21321167X-RAY DIFFRACTION88
2.0646-2.13820.22381370.18981246X-RAY DIFFRACTION93
2.1382-2.22370.24051430.17191254X-RAY DIFFRACTION94
2.2237-2.32470.22631370.16641251X-RAY DIFFRACTION94
2.3247-2.4470.2111500.15771276X-RAY DIFFRACTION95
2.447-2.59980.19251400.15441321X-RAY DIFFRACTION97
2.5998-2.79990.20071490.1511327X-RAY DIFFRACTION98
2.7999-3.08030.1881520.15351348X-RAY DIFFRACTION99
3.0803-3.52310.19991480.14711365X-RAY DIFFRACTION100
3.5231-4.42750.18351560.13811375X-RAY DIFFRACTION100
4.4275-17.8480.19841640.16661443X-RAY DIFFRACTION100

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