+Open data
-Basic information
Entry | Database: PDB / ID: 4uav | ||||||
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Title | Crystal structure of CbbY (AT3G48420) from Arabidobsis thaliana | ||||||
Components | Haloacid dehalogenase-like hydrolase domain-containing protein At3g48420 | ||||||
Keywords | HYDROLASE / haloacid dehalogenase (HAD) hydrolase superfamily / phosphatase | ||||||
Function / homology | Function and homology information Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / chloroplast envelope / chloroplast stroma / chloroplast / hydrolase activity / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å | ||||||
Authors | Bracher, A. / Sharma, A. / Starling-Windhof, A. / Hartl, F.U. / Hayer-Hartl, M. | ||||||
Citation | Journal: Nat.Plants / Year: 2015 Title: Degradation of potent Rubisco inhibitor by selective sugar phosphatase. Authors: Bracher, A. / Sharma, A. / Starling-Windhof, A. / Hartl, F.U. / Hayer-Hartl, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4uav.cif.gz | 127.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uav.ent.gz | 97.7 KB | Display | PDB format |
PDBx/mmJSON format | 4uav.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ua/4uav ftp://data.pdbj.org/pub/pdb/validation_reports/ua/4uav | HTTPS FTP |
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-Related structure data
Related structure data | 4uarSC 4uasC 4uatC 4uauC 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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Details | biological unit is a monomer |
-Components
#1: Protein | Mass: 26778.793 Da / Num. of mol.: 1 / Fragment: UNP residues 74-319 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At3g48420, T29H11.60 / Plasmid: pHue / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q94K71, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases |
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#2: Chemical | ChemComp-MG / |
#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: 2.72 Å3/Da / Density % sol: 54.74 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 25 % (wt/vol) PEG-6000 and 0.1 M Tris-HCl pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 27, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.3→70.021 Å / Num. all: 70347 / Num. obs: 70347 / % possible obs: 97.9 % / Redundancy: 3.7 % / Rpim(I) all: 0.029 / Rrim(I) all: 0.058 / Rsym value: 0.049 / Net I/av σ(I): 9.566 / Net I/σ(I): 13.2 / Num. measured all: 257575 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4UAR Resolution: 1.3→30 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.966 / WRfactor Rfree: 0.1673 / WRfactor Rwork: 0.1331 / FOM work R set: 0.9146 / SU B: 1.431 / SU ML: 0.027 / SU R Cruickshank DPI: 0.0406 / SU Rfree: 0.0426 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.041 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 118.61 Å2 / Biso mean: 17.581 Å2 / Biso min: 7.41 Å2
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Refinement step | Cycle: final / Resolution: 1.3→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.3→1.334 Å / Total num. of bins used: 20
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