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Yorodumi- PDB-4uau: Crystal structure of CbbY (mutant D10N) from Rhodobacter sphaeroi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4uau | ||||||
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Title | Crystal structure of CbbY (mutant D10N) from Rhodobacter sphaeroides in complex with Xylulose-(1,5)bisphosphate, crystal form II | ||||||
Components | Protein CbbY | ||||||
Keywords | HYDROLASE / haloacid dehalogenase (HAD) hydrolase superfamily / phosphatase | ||||||
Function / homology | Function and homology information xylulose catabolic process / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / hydrolase activity / magnesium ion binding Similarity search - Function | ||||||
Biological species | Rhodobacter sphaeroides (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 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 | 4uau.cif.gz | 119 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uau.ent.gz | 89.7 KB | Display | PDB format |
PDBx/mmJSON format | 4uau.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ua/4uau ftp://data.pdbj.org/pub/pdb/validation_reports/ua/4uau | HTTPS FTP |
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-Related structure data
Related structure data | 4uarSC 4uasC 4uatC 4uavC 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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2 |
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Unit cell |
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Details | biological unit is a monomer |
-Components
#1: Protein | Mass: 25150.752 Da / Num. of mol.: 2 / Mutation: D10N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: cbbY / Plasmid: pHue / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P95649 #2: Sugar | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.02 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 25 % PEG-1000, 0.1 M MES-NaOH pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.97639 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 7, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97639 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.45→46.715 Å / Num. all: 80244 / Num. obs: 80244 / % possible obs: 99.2 % / Redundancy: 6.3 % / Rpim(I) all: 0.028 / Rrim(I) all: 0.071 / Rsym value: 0.065 / Net I/av σ(I): 10.533 / Net I/σ(I): 17 / Num. measured all: 502549 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.45→30 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.1953 / WRfactor Rwork: 0.1635 / FOM work R set: 0.8686 / SU B: 1.28 / SU ML: 0.049 / SU R Cruickshank DPI: 0.0706 / SU Rfree: 0.0735 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.071 / ESU R Free: 0.074 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 100.92 Å2 / Biso mean: 23.354 Å2 / Biso min: 11.61 Å2
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Refinement step | Cycle: final / Resolution: 1.45→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.488 Å / Total num. of bins used: 20
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