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Yorodumi- PDB-5had: Crystal structure of intermembrane space region of chloroplast pr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5had | |||||||||
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Title | Crystal structure of intermembrane space region of chloroplast protein ARC6 | |||||||||
Components | Protein ACCUMULATION AND REPLICATION OF CHLOROPLASTS 6, chloroplastic | |||||||||
Keywords | PHOTOSYNTHESIS / intermembrane space / chloroplast | |||||||||
Function / homology | Function and homology information response to gibberellin / chloroplast inner membrane / chloroplast organization / chloroplast fission / chloroplast envelope / plastid / chloroplast / : / protein homodimerization activity Similarity search - Function | |||||||||
Biological species | Arabidopsis thaliana (thale cress) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.238 Å | |||||||||
Authors | Feng, Y. / Yu, X. | |||||||||
Funding support | China, 2items
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Citation | Journal: Nat Plants / Year: 2017 Title: Structural insights into the coordination of plastid division by the ARC6-PDV2 complex Authors: Wang, W. / Li, J. / Sun, Q. / Yu, X. / Zhang, W. / Jia, N. / An, C. / Li, Y. / Dong, Y. / Han, F. / Chang, N. / Liu, X. / Zhu, Z. / Yu, Y. / Fan, S. / Yang, M. / Luo, S.Z. / Gao, H. / Feng, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5had.cif.gz | 68.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5had.ent.gz | 49.8 KB | Display | PDB format |
PDBx/mmJSON format | 5had.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5had_validation.pdf.gz | 443 KB | Display | wwPDB validaton report |
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Full document | 5had_full_validation.pdf.gz | 444 KB | Display | |
Data in XML | 5had_validation.xml.gz | 7.8 KB | Display | |
Data in CIF | 5had_validation.cif.gz | 9.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ha/5had ftp://data.pdbj.org/pub/pdb/validation_reports/ha/5had | HTTPS FTP |
-Related 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: 18939.193 Da / Num. of mol.: 1 Fragment: Interaction with PDV2 domain, UNP residues 646-801 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ARC6, At5g42480, MDH9.18 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9FIG9 | ||
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#2: Chemical | ChemComp-EDO / #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: 2.56 Å3/Da / Density % sol: 51.87 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / Details: ethylene glycol / PH range: 5.6 - 6.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 2, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.238→50 Å / Num. obs: 9790 / % possible obs: 100 % / Redundancy: 15.3 % / Net I/σ(I): 68.8 |
Reflection shell | Resolution: 2.24→2.28 Å / Mean I/σ(I) obs: 13.9 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.238→28.718 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.77 / 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: 2.238→28.718 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -21.9992 Å / Origin y: 22.6062 Å / Origin z: -19.6833 Å
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Refinement TLS group | Selection details: all |