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- PDB-3v9r: Crystal structure of Saccharomyces cerevisiae MHF complex -

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Basic information

Entry
Database: PDB / ID: 3v9r
TitleCrystal structure of Saccharomyces cerevisiae MHF complex
Components
  • Uncharacterized protein YDL160C-A
  • Uncharacterized protein YOL086W-A
KeywordsDNA BINDING PROTEIN / MHF1 / MHF2 / histone fold / Fanconi anemia / DNA repair
Function / homology
Function and homology information


FANCM-MHF complex / resolution of meiotic recombination intermediates / kinetochore assembly / replication fork processing / protein heterodimerization activity / DNA repair / DNA damage response / chromatin binding / DNA binding
Similarity search - Function
Centromere protein X / CENP-S/Mhf1 / CENP-S associating Centromere protein X / CENP-S protein / Histone, subunit A / Histone, subunit A / Histone-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Inner kinetochore subunit MHF2 / Inner kinetochore subunit MHF1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsYang, H. / Zhang, T. / Zhong, C. / Li, H. / Zhou, J. / Ding, J.
CitationJournal: Structure / Year: 2012
Title: Saccharomyces Cerevisiae MHF Complex Structurally Resembles the Histones (H3-H4)(2) Heterotetramer and Functions as a Heterotetramer
Authors: Yang, H. / Zhang, T. / Tao, Y. / Wu, L. / Li, H.T. / Zhou, J.Q. / Zhong, C. / Ding, J.
History
DepositionDec 28, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein YOL086W-A
B: Uncharacterized protein YDL160C-A
C: Uncharacterized protein YOL086W-A
D: Uncharacterized protein YDL160C-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2385
Polymers42,1424
Non-polymers961
Water90150
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.823, 104.065, 70.862
Angle α, β, γ (deg.)90.000, 109.090, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Uncharacterized protein YOL086W-A / MHF1


Mass: 10703.676 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: YOL086W-A / Plasmid: pETDuet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus / References: UniProt: Q3E835
#2: Protein Uncharacterized protein YDL160C-A / MHF2


Mass: 10367.110 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: YDL160C-A / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus / References: UniProt: Q3E829
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.85 Å3/Da / Density % sol: 56.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.6M (NH4)2SO4, 3% isopropanol, 8% polypropylene glycol P400, 0.02M CaCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9786 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jun 29, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 18254 / % possible obs: 98.6 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 47.6
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 6.8 / % possible all: 98

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.902 / Occupancy max: 1 / Occupancy min: 1 / SU B: 21.17 / SU ML: 0.227 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2904 933 5.1 %RANDOM
Rwork0.2394 ---
obs0.2421 18206 98.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 260.94 Å2 / Biso mean: 69.0121 Å2 / Biso min: 2.66 Å2
Baniso -1Baniso -2Baniso -3
1-3.2 Å20 Å21.71 Å2
2---0.34 Å20 Å2
3----1.74 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2594 0 5 50 2649
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222624
X-RAY DIFFRACTIONr_angle_refined_deg1.0521.993520
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1195314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.7424.925134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.12315532
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9451522
X-RAY DIFFRACTIONr_chiral_restr0.0690.2402
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021916
X-RAY DIFFRACTIONr_mcbond_it4.9091.51586
X-RAY DIFFRACTIONr_mcangle_it8.71122544
X-RAY DIFFRACTIONr_scbond_it9.99331038
X-RAY DIFFRACTIONr_scangle_it13.6914.5976
X-RAY DIFFRACTIONr_rigid_bond_restr5.71232624
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 79 -
Rwork0.275 1266 -
all-1345 -
obs--97.82 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.14090.01080.1272-0.06490.05630.07230.0245-0.04880.0224-0.0346-0.0360.01830.002-0.05010.01150.12380.00950.03280.09590.01320.050438.588315.534121.7831
20.1942-0.39480.07650.3770.20090.443-0.06850.0596-0.01370.1188-0.0470.05050.1650.00490.11550.1409-0.02620.04170.0598-0.01280.068636.488316.503524.5767
31.140.1297-0.9780.0826-0.28030.93060.13340.06750.07550.0179-0.0234-0.0154-0.1181-0.0511-0.110.13150.00970.04260.093-0.0010.051213.896236.17814.4032
40.13690.1227-0.23750.05850.0410.9255-0.02280.0408-0.02910.02350.0028-0.03140.0136-0.05490.02010.1348-0.00050.04640.08270.01090.056712.039934.3817.3306
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 89
2X-RAY DIFFRACTION2B1 - 84
3X-RAY DIFFRACTION3C3 - 89
4X-RAY DIFFRACTION4D1 - 80

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