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- PDB-2aql: Crystal Structure of the MRG15 MRG domain -

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Basic information

Entry
Database: PDB / ID: 2aql
TitleCrystal Structure of the MRG15 MRG domain
ComponentsMortality factor 4-like protein 1
KeywordsDNA BINDING PROTEIN / helix hairpins / MRG domain / core binding domain / recombinase / DNA binding / chromatin remodeling
Function / homology
Function and homology information


regulation of double-strand break repair / Sin3-type complex / NuA4 histone acetyltransferase complex / positive regulation of double-strand break repair via homologous recombination / double-strand break repair via homologous recombination / nucleosome / chromatin organization / HATs acetylate histones / regulation of apoptotic process / regulation of cell cycle ...regulation of double-strand break repair / Sin3-type complex / NuA4 histone acetyltransferase complex / positive regulation of double-strand break repair via homologous recombination / double-strand break repair via homologous recombination / nucleosome / chromatin organization / HATs acetylate histones / regulation of apoptotic process / regulation of cell cycle / nuclear speck / positive regulation of DNA-templated transcription / nucleoplasm
Similarity search - Function
MRG domain / MRG / MRG domain / MRG, C-terminal domain superfamily / MRG / MRG domain profile. / Enzyme I; Chain A, domain 2 / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / Chromo-like domain superfamily ...MRG domain / MRG / MRG domain / MRG, C-terminal domain superfamily / MRG / MRG domain profile. / Enzyme I; Chain A, domain 2 / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / Chromo-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Mortality factor 4-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsQuiocho, F.A. / Bowman, B.R.
CitationJournal: Structure / Year: 2006
Title: Multipurpose MRG domain involved in cell senescence and proliferation exhibits structural homology to a DNA-interacting domain.
Authors: Bowman, B.R. / Moure, C.M. / Kirtane, B.M. / Welschhans, R.L. / Tominaga, K. / Pereira-Smith, O.M. / Quiocho, F.A.
History
DepositionAug 18, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Mortality factor 4-like protein 1
B: Mortality factor 4-like protein 1


Theoretical massNumber of molelcules
Total (without water)40,1442
Polymers40,1442
Non-polymers00
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-17 kcal/mol
Surface area15860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.200, 111.200, 84.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Mortality factor 4-like protein 1 / MORF-related gene 15 protein / Transcription factor-like protein MRG15 / MSL3-1 protein


Mass: 20072.080 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MORF4L1, MRG15 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UBU8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O

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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: 2.5 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: PEG 10000, cacodylate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97916 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionBiso Wilson estimate: 22.3 Å2

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→41.86 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 527077.68 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1666 9.9 %RANDOM
Rwork0.245 ---
all0.273 ---
obs0.245 16841 97 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.7994 Å2 / ksol: 0.380984 e/Å3
Displacement parametersBiso mean: 36.7 Å2
Baniso -1Baniso -2Baniso -3
1--2.69 Å21.87 Å20 Å2
2---2.69 Å20 Å2
3---5.39 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.3→41.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2545 0 0 103 2648
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.306 269 9.9 %
Rwork0.275 2459 -
obs--94.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param

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