+Open data
-Basic information
Entry | Database: PDB / ID: 5.0E+37 | |||||||||
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Title | Redox protein from Chlamydomonas reinhardtii | |||||||||
Components | EF-Hand domain-containing thioredoxin | |||||||||
Keywords | OXIDOREDUCTASE / Calredoxin / calcium- / redox- / Chlamydomonas reinhardtii | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Chlamydomonas reinhardtii (plant) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | |||||||||
Authors | Charoenwattansatien, R. / Hochmal, A.K. / Zinzius, K. / Muto, R. / Tanaka, H. / Hippler, M. / Kurisu, G. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Nat Commun / Year: 2016 Title: Calredoxin represents a novel type of calcium-dependent sensor-responder connected to redox regulation in the chloroplast Authors: Hochmal, A.K. / Zinzius, K. / Charoenwattanasatien, R. / Gabelein, P. / Mutoh, R. / Tanaka, H. / Schulze, S. / Liu, G. / Scholz, M. / Nordhues, A. / Offenborn, J.N. / Petroutsos, D. / ...Authors: Hochmal, A.K. / Zinzius, K. / Charoenwattanasatien, R. / Gabelein, P. / Mutoh, R. / Tanaka, H. / Schulze, S. / Liu, G. / Scholz, M. / Nordhues, A. / Offenborn, J.N. / Petroutsos, D. / Finazzi, G. / Fufezan, C. / Huang, K. / Kurisu, G. / Hippler, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5e37.cif.gz | 154.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5e37.ent.gz | 124 KB | Display | PDB format |
PDBx/mmJSON format | 5e37.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e3/5e37 ftp://data.pdbj.org/pub/pdb/validation_reports/e3/5e37 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 39950.398 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: CHLREDRAFT_205510 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: A8IXH4*PLUS #2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEB | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.97 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 1.5 M LiSO4 in 0.1 M MES-NaOH buffer pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Apr 22, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 108097 / % possible obs: 99.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 35.3 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.558 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.794 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.518 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→50 Å
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Refine LS restraints |
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