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- PDB-2f5k: Crystal structure of the chromo domain of human MRG15 -

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Basic information

Entry
Database: PDB / ID: 2f5k
TitleCrystal structure of the chromo domain of human MRG15
ComponentsMortality factor 4-like protein 1
KeywordsGENE REGULATION / beta barrel
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 / HATs acetylate histones / chromatin organization / fibroblast proliferation / regulation of apoptotic process ...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 / HATs acetylate histones / chromatin organization / fibroblast proliferation / regulation of apoptotic process / regulation of cell cycle / nuclear speck / chromatin binding / positive regulation of DNA-templated transcription / nucleoplasm
Similarity search - Function
MRG / MRG domain / MRG, C-terminal domain superfamily / MRG / MRG domain profile. / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / SH3 type barrels. - #140 / Chromo-like domain superfamily / SH3 type barrels. ...MRG / MRG domain / MRG, C-terminal domain superfamily / MRG / MRG domain profile. / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / SH3 type barrels. - #140 / Chromo-like domain superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Mortality factor 4-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsZhang, P. / Du, J. / Ding, J.
CitationJournal: Nucleic Acids Res. / Year: 2006
Title: Structure of human MRG15 chromo domain and its binding to Lys36-methylated histone H3.
Authors: Zhang, P. / Du, J. / Sun, B. / Dong, X. / Xu, G. / Zhou, J. / Huang, Q. / Liu, Q. / Hao, Q. / Ding, J.
History
DepositionNov 26, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 14, 2006Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 18, 2019Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_src_gen.gene_src_common_name ..._entity.pdbx_description / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_db_isoform / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_accession_code / _struct_ref_seq_dif.pdbx_seq_db_name
Revision 1.4Mar 13, 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
C: Mortality factor 4-like protein 1
D: Mortality factor 4-like protein 1
E: Mortality factor 4-like protein 1
F: Mortality factor 4-like protein 1


Theoretical massNumber of molelcules
Total (without water)73,5076
Polymers73,5076
Non-polymers00
Water8,233457
1
A: Mortality factor 4-like protein 1


Theoretical massNumber of molelcules
Total (without water)12,2511
Polymers12,2511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mortality factor 4-like protein 1


Theoretical massNumber of molelcules
Total (without water)12,2511
Polymers12,2511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Mortality factor 4-like protein 1


Theoretical massNumber of molelcules
Total (without water)12,2511
Polymers12,2511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Mortality factor 4-like protein 1


Theoretical massNumber of molelcules
Total (without water)12,2511
Polymers12,2511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Mortality factor 4-like protein 1


Theoretical massNumber of molelcules
Total (without water)12,2511
Polymers12,2511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Mortality factor 4-like protein 1


Theoretical massNumber of molelcules
Total (without water)12,2511
Polymers12,2511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.480, 80.313, 81.285
Angle α, β, γ (deg.)90.00, 123.91, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Mortality factor 4-like protein 1 / MORF-related gene 15 isoform 1


Mass: 12251.144 Da / Num. of mol.: 6 / Fragment: chromo domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MORF4L1, MRG15, FWP006, HSPC008, HSPC061, PP368 / Plasmid: pET-3E-His / 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.: 457 / 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: 2.02 Å3/Da / Density % sol: 39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 14% PEG 3350, 0.2M potassium nitrate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONCHESS F210.9793
SYNCHROTRONCHESS F120.9124
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDJul 14, 2005
ADSC QUANTUM 42CCDJul 14, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.91241
ReflectionResolution: 2.2→50 Å / Num. all: 29640 / Num. obs: 29581 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.2→2.28 Å / % possible all: 99.6

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Processing

Software
NameVersionClassificationNB
REFMAC5refinement
PDB_EXTRACT1.701data extraction
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.908 / WRfactor Rfree: 0.247 / SU B: 20.364 / SU ML: 0.212 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2727 1485 5 %RANDOM
Rwork0.22447 ---
all0.227 29667 --
obs0.22697 28095 99.71 %-
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: 52.674 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å2-1.38 Å2
2---1.04 Å20 Å2
3----0.4 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4114 0 0 457 4571
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0214231
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5231.9355695
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7393477
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.1115818
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.110.2559
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023257
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2870.32054
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2720.5589
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3190.349
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2070.517
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5281.52418
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.70123897
X-RAY DIFFRACTIONr_scbond_it2.17431813
X-RAY DIFFRACTIONr_scangle_it3.4574.51798
X-RAY DIFFRACTIONr_rigid_bond_restr1.49624231
X-RAY DIFFRACTIONr_sphericity_free2.7762457
X-RAY DIFFRACTIONr_sphericity_bonded1.65224119
LS refinement shellResolution: 2.202→2.259 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.348 98
Rwork0.262 2036
obs-2134

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