+Open data
-Basic information
Entry | Database: PDB / ID: 4uar | ||||||
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Title | Crystal structure of apo-CbbY from Rhodobacter sphaeroides | ||||||
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 / SAD / SIRAS / Resolution: 1.9 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 | 4uar.cif.gz | 59.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uar.ent.gz | 42 KB | Display | PDB format |
PDBx/mmJSON format | 4uar.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4uar_validation.pdf.gz | 433.1 KB | Display | wwPDB validaton report |
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Full document | 4uar_full_validation.pdf.gz | 433.4 KB | Display | |
Data in XML | 4uar_validation.xml.gz | 11.7 KB | Display | |
Data in CIF | 4uar_validation.cif.gz | 16.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ua/4uar ftp://data.pdbj.org/pub/pdb/validation_reports/ua/4uar | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | biological unit is the same as asym. |
-Components
#1: Protein | Mass: 25151.736 Da / Num. of mol.: 1 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 |
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#2: Chemical | ChemComp-GOL / |
#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: 3.03 Å3/Da / Density % sol: 59.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 16-20 % PEG-6000 and 0.1 M Hepes-NaOH pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97138 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 25, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97138 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 13.4 % / Number: 101392 / Rsym value: 0.151 / D res high: 2.796 Å / D res low: 41.734 Å / Num. obs: 7592 / % possible obs: 100 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.9→41.608 Å / Num. all: 24048 / Num. obs: 24048 / % possible obs: 99.8 % / Redundancy: 6.5 % / Rpim(I) all: 0.023 / Rrim(I) all: 0.059 / Rsym value: 0.05 / Net I/av σ(I): 10.75 / Net I/σ(I): 19.5 / Num. measured all: 156631 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: SIRAS | |||||||||||||||||||||||||||||||||||||||||||||||||
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Phasing dm | FOM : 0.52 / FOM acentric: 0.51 / FOM centric: 0.85 / Reflection: 22898 / Reflection acentric: 22221 / Reflection centric: 677 | |||||||||||||||||||||||||||||||||||||||||||||||||
Phasing dm shell |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.2215 / WRfactor Rwork: 0.1963 / FOM work R set: 0.8583 / SU B: 2.899 / SU ML: 0.086 / SU R Cruickshank DPI: 0.1347 / SU Rfree: 0.1241 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.124 / 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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 75.07 Å2 / Biso mean: 28.125 Å2 / Biso min: 16.45 Å2
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Refinement step | Cycle: final / Resolution: 1.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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