+Open data
-Basic information
Entry | Database: PDB / ID: 5iz3 | ||||||
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Title | P. patens sedoheptulose-1,7-bisphosphatase | ||||||
Components |
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Keywords | HYDROLASE / Physcomitrella patens carbon metabolism sedoheptulose bisphophatase | ||||||
Function / homology | Function and homology information phosphatase activity / carbohydrate metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | Physcomitrella patens (plant) Physcomitrella patens subsp. patens (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Einsle, O. / Guetle, D. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2016 Title: Chloroplast FBPase and SBPase are thioredoxin-linked enzymes with similar architecture but different evolutionary histories. Authors: Gutle, D.D. / Roret, T. / Muller, S.J. / Couturier, J. / Lemaire, S.D. / Hecker, A. / Dhalleine, T. / Buchanan, B.B. / Reski, R. / Einsle, O. / Jacquot, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5iz3.cif.gz | 265.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5iz3.ent.gz | 213.5 KB | Display | PDB format |
PDBx/mmJSON format | 5iz3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iz/5iz3 ftp://data.pdbj.org/pub/pdb/validation_reports/iz/5iz3 | HTTPS FTP |
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-Related structure data
Related structure data | 5iz1C 1d9qS 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: 34655.113 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Physcomitrella patens (plant) / Gene: PHYPADRAFT_122707 / Production host: Physcomitrella patens (plant) / References: UniProt: A9S1S8 | ||||
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#2: Protein | Mass: 34685.137 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Physcomitrella patens subsp. patens (plant) Gene: PHYPADRAFT_122707 / Production host: Physcomitrella patens (plant) / References: UniProt: A9S1S8 | ||||
#3: Chemical | #4: Chemical | #5: 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: 2.26 Å3/Da / Density % sol: 45.66 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 40 % PEG 600 0.2 M imidazole/malate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0001 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 10, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0001 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→100 Å / Num. obs: 155382 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Redundancy: 10.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Net I/σ(I): 30.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1D9Q Resolution: 1.3→98.62 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.797 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.058 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.237 Å2
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Refinement step | Cycle: 1 / Resolution: 1.3→98.62 Å
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Refine LS restraints |
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