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- PDB-2f5j: Crystal structure of MRG domain from human MRG15 -

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Basic information

Entry
Database: PDB / ID: 2f5j
TitleCrystal structure of MRG domain from human MRG15
ComponentsMortality factor 4-like protein 1
KeywordsGENE REGULATION / MRG fold / mainly a-helix
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: 2.2 Å
AuthorsZhang, P. / Du, J. / Ding, J.
CitationJournal: Protein Sci. / Year: 2006
Title: The MRG domain of human MRG15 uses a shallow hydrophobic pocket to interact with the N-terminal region of PAM14
Authors: Zhang, P. / Zhao, J. / Wang, B. / Du, J. / Lu, Y. / Chen, J. / Ding, J.
History
DepositionNov 26, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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)42,2862
Polymers42,2862
Non-polymers00
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-19 kcal/mol
Surface area16190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.151, 111.151, 86.991
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: 21143.234 Da / Num. of mol.: 2 / Fragment: MRG domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-22B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9UBU8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.44 Å3/Da / Density % sol: 49.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 20% PEG 4000, 0.1M HEPES, 5% iso-propanol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-6A11
SYNCHROTRONPhoton Factory BL-18B20.9782, 0.9819, 0.9875
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDMar 10, 2004
ADSC QUANTUM 42CCDMar 10, 2004
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97821
30.98191
40.98751
ReflectionResolution: 2.2→50 Å / Num. all: 21311 / Num. obs: 20198 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 %
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4 % / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT1.701data extraction
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.914 / SU B: 5.128 / SU ML: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24323 1005 5 %RANDOM
Rwork0.20458 ---
all0.219 21311 --
obs0.20653 19177 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 48.134 Å2
Baniso -1Baniso -2Baniso -3
1--1.98 Å2-0.99 Å20 Å2
2---1.98 Å20 Å2
3---2.97 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2598 0 0 238 2836
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222670
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.541.9773625
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6255312
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1050.2396
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022019
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2530.21472
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2240.2229
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.240.230
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.210.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6451.51590
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.0422566
X-RAY DIFFRACTIONr_scbond_it3.29631080
X-RAY DIFFRACTIONr_scangle_it5.3764.51059
X-RAY DIFFRACTIONr_rigid_bond_restr1.86122670
X-RAY DIFFRACTIONr_sphericity_free3.3582238
X-RAY DIFFRACTIONr_sphericity_bonded1.96122600
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.28 71
Rwork0.221 1414

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