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Yorodumi- PDB-8waf: Crystal structure of the C-terminal fragment (residues 756-982 wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8waf | |||||||||||||||
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Title | Crystal structure of the C-terminal fragment (residues 756-982 with the C864S mutation) of Arabidopsis thaliana CHUP1 | |||||||||||||||
Components | Protein CHUP1, chloroplastic | |||||||||||||||
Keywords | PLANT PROTEIN / Actin / Actin nucleator / Chloroplast movement / CHLOROPLAST UNUSUAL POSITIONING 1 | |||||||||||||||
Function / homology | Protein CHUP1-like / chloroplast relocation / chloroplast outer membrane / chloroplast / cytosol / Protein CHUP1, chloroplastic Function and homology information | |||||||||||||||
Biological species | Arabidopsis thaliana (thale cress) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å | |||||||||||||||
Authors | Shimada, A. / Takano, A. / Nakamura, Y. / Kohda, D. | |||||||||||||||
Funding support | Japan, 4items
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Citation | Journal: Plant Cell / Year: 2024 Title: CHLOROPLAST UNUSUAL POSITIONING 1 is a plant-specific actin polymerization factor regulating chloroplast movement. Authors: Kong, S.G. / Yamazaki, Y. / Shimada, A. / Kijima, S.T. / Hirose, K. / Katoh, K. / Ahn, J. / Song, H.G. / Han, J.W. / Higa, T. / Takano, A. / Nakamura, Y. / Suetsugu, N. / Kohda, D. / Uyeda, T.Q.P. / Wada, M. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8waf.cif.gz | 106.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8waf.ent.gz | 81.9 KB | Display | PDB format |
PDBx/mmJSON format | 8waf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8waf_validation.pdf.gz | 429.6 KB | Display | wwPDB validaton report |
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Full document | 8waf_full_validation.pdf.gz | 431.7 KB | Display | |
Data in XML | 8waf_validation.xml.gz | 9.8 KB | Display | |
Data in CIF | 8waf_validation.cif.gz | 12.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wa/8waf ftp://data.pdbj.org/pub/pdb/validation_reports/wa/8waf | HTTPS FTP |
-Related structure data
Related structure data | 8wagC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 26482.100 Da / Num. of mol.: 1 / Mutation: C864S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CHUP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9LI74 |
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#2: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 6.67 Å3/Da / Density % sol: 81.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 50mM CHES (pH 9.0), 0.2M lithium sulfate, 36% PEG400 |
-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: 0.97892 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jul 16, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97892 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 18407 / % possible obs: 99.9 % / Redundancy: 41.9 % / Rmerge(I) obs: 0.201 / Rpim(I) all: 0.032 / Rrim(I) all: 0.204 / Χ2: 1.032 / Net I/σ(I): 5.5 / Num. measured all: 770816 |
Reflection shell | Resolution: 2.8→2.85 Å / Num. unique obs: 882 / CC1/2: 0.836 / Rpim(I) all: 0.512 / Χ2: 1.016 / % possible all: 100 |
-Phasing
Phasing | Method: SAD |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.8→44.486 Å / FOM work R set: 0.8123 / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.48 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 274.63 Å2 / Biso mean: 71.92 Å2 / Biso min: 37.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.8→44.486 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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