+Open data
-Basic information
Entry | Database: PDB / ID: 7da0 | |||||||||
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Title | High-resolution crystal structure of the chicken MHF complex | |||||||||
Components |
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Keywords | DNA BINDING PROTEIN / histone fold / DNA binding / DNA repair / nucleus | |||||||||
Function / homology | Function and homology information PKR-mediated signaling / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Resolution of Sister Chromatid Cohesion / EML4 and NUDC in mitotic spindle formation / RHO GTPases Activate Formins / Separation of Sister Chromatids / Deposition of new CENPA-containing nucleosomes at the centromere / Fanconi Anemia Pathway / FANCM-MHF complex / Fanconi anaemia nuclear complex ...PKR-mediated signaling / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Resolution of Sister Chromatid Cohesion / EML4 and NUDC in mitotic spindle formation / RHO GTPases Activate Formins / Separation of Sister Chromatids / Deposition of new CENPA-containing nucleosomes at the centromere / Fanconi Anemia Pathway / FANCM-MHF complex / Fanconi anaemia nuclear complex / resolution of meiotic recombination intermediates / kinetochore assembly / replication fork processing / kinetochore / protein heterodimerization activity / cell division / DNA repair / chromatin binding / DNA binding Similarity search - Function | |||||||||
Biological species | Gallus gallus (chicken) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å | |||||||||
Authors | Ito, S. / Nishino, T. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2021 Title: Structural analysis of the chicken FANCM-MHF complex and its stability. Authors: Ito, S. / Nishino, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7da0.cif.gz | 104.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7da0.ent.gz | 65.1 KB | Display | PDB format |
PDBx/mmJSON format | 7da0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/da/7da0 ftp://data.pdbj.org/pub/pdb/validation_reports/da/7da0 | HTTPS FTP |
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-Related structure data
Related structure data | 7da1C 7da2C 3b0bS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 11875.330 Da / Num. of mol.: 1 / Mutation: C26A, C28A, C55A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: CENPS, APITD1 / Plasmid: pRSFDUET / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E1BSW7 |
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#2: Protein | Mass: 9361.746 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: CENPX, STRA13 / Plasmid: pRSFDUET / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DJH7 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 37.01 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M Tris-Bicine pH 8.5, 0.1 M Carboxylic acids mix, 12.5% MPD, 12.5% PEG 1000, 12.5% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 18, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→34.01 Å / Num. obs: 43638 / % possible obs: 96.74 % / Redundancy: 3.7 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.0056 / Rpim(I) all: 0.034 / Rrim(I) all: 0.066 / Net I/σ(I): 36.64 |
Reflection shell | Resolution: 1.25→1.295 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.851 / Mean I/σ(I) obs: 2.17 / Num. unique obs: 4340 / Rpim(I) all: 0.52 / Rrim(I) all: 0.999 / % possible all: 96.21 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3B0B Resolution: 1.25→34.01 Å / SU ML: 0.1362 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.8617 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.88 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.25→34.01 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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