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Yorodumi- PDB-5wjc: Crystal structure of Schizosaccharomyces pombe Mis16 in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wjc | |||||||||||||||
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Title | Crystal structure of Schizosaccharomyces pombe Mis16 in complex with Eic1 | |||||||||||||||
Components |
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Keywords | PROTEIN BINDING / Fission yeast chaperone for histone H4 / Subcomponent of Mis18 complex / Eic1 binding / WD-40 repeats domain | |||||||||||||||
Function / homology | Function and homology information HATs acetylate histones / RMTs methylate histone arginines / CENP-A recruiting complex / Neddylation / HDACs deacetylate histones / H3-H4 histone complex chaperone activity / chromosome, centromeric core domain / Rpd3L complex / Rpd3L-Expanded complex / CENP-A containing chromatin assembly ...HATs acetylate histones / RMTs methylate histone arginines / CENP-A recruiting complex / Neddylation / HDACs deacetylate histones / H3-H4 histone complex chaperone activity / chromosome, centromeric core domain / Rpd3L complex / Rpd3L-Expanded complex / CENP-A containing chromatin assembly / protein localization to chromosome, centromeric region / attachment of mitotic spindle microtubules to kinetochore / NuRD complex / ESC/E(Z) complex / mitotic sister chromatid segregation / chromosome, centromeric region / nucleosome binding / kinetochore / histone binding / chromatin remodeling / cell division / regulation of DNA-templated transcription / nucleoplasm / nucleus / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Schizosaccharomyces pombe 972h- (yeast) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.298 Å | |||||||||||||||
Authors | An, S. / Cho, U.-S. / Koldewey, P. / Chik, J. / Subramanian, L. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: Structure / Year: 2018 Title: Mis16 Switches Function from a Histone H4 Chaperone to a CENP-ACnp1-Specific Assembly Factor through Eic1 Interaction. Authors: An, S. / Koldewey, P. / Chik, J. / Subramanian, L. / Cho, U.S. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wjc.cif.gz | 98.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wjc.ent.gz | 72.6 KB | Display | PDB format |
PDBx/mmJSON format | 5wjc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5wjc_validation.pdf.gz | 433.2 KB | Display | wwPDB validaton report |
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Full document | 5wjc_full_validation.pdf.gz | 435.3 KB | Display | |
Data in XML | 5wjc_validation.xml.gz | 17 KB | Display | |
Data in CIF | 5wjc_validation.cif.gz | 24 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wj/5wjc ftp://data.pdbj.org/pub/pdb/validation_reports/wj/5wjc | HTTPS FTP |
-Related structure data
Related structure data | 4xyhS S: Starting model for refinement |
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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
#1: Protein | Mass: 48481.555 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe 972h- (yeast) Strain: 972 / ATCC 24843 / Gene: mis16, hat2, SPCC1672.10 / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: O94244 |
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#2: Protein | Mass: 13453.742 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe 972h- (yeast) Strain: 972 / ATCC 24843 / Gene: SPBC27B12.02, SPBC30B4.10 / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: O42995 |
#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: 2.58 Å3/Da / Density % sol: 52.24 % / Description: Thick needle |
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Crystal grow | Temperature: 296.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 100 mM Tris-HCl pH 8.5, 25% PEG 2000MME |
-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 26459 / % possible obs: 90.8 % / Redundancy: 8 % / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.035 / Net I/σ(I): 22.4 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 4 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1698 / Rpim(I) all: 0.39 / % possible all: 59.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4XYH Resolution: 2.298→48.886 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.12 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.298→48.886 Å
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Refine LS restraints |
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LS refinement shell |
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