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Yorodumi- PDB-4uas: Crystal structure of CbbY from Rhodobacter sphaeroides in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4uas | ||||||
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Title | Crystal structure of CbbY from Rhodobacter sphaeroides in complex with phosphate | ||||||
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: 1.2 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 | 4uas.cif.gz | 234.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uas.ent.gz | 187.2 KB | Display | PDB format |
PDBx/mmJSON format | 4uas.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4uas_validation.pdf.gz | 462.7 KB | Display | wwPDB validaton report |
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Full document | 4uas_full_validation.pdf.gz | 468.8 KB | Display | |
Data in XML | 4uas_validation.xml.gz | 28.9 KB | Display | |
Data in CIF | 4uas_validation.cif.gz | 45.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ua/4uas ftp://data.pdbj.org/pub/pdb/validation_reports/ua/4uas | HTTPS FTP |
-Related structure data
Related structure data | 4uarSC 4uatC 4uauC 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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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 1 - 225 / Label seq-ID: 1 - 225
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Details | biological unit is a monomer |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 25151.736 Da / Num. of mol.: 2 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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-Non-polymers , 5 types, 834 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: 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: 2.29 Å3/Da / Density % sol: 46.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 10 mM fructose-1,6-bisphosphate, 22 % PEG-6000 and 0.1 M MES-HCl pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99987 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 22, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.99987 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.2→46.971 Å / Num. all: 142564 / Num. obs: 142564 / % possible obs: 97.8 % / Redundancy: 4.3 % / Rpim(I) all: 0.025 / Rrim(I) all: 0.054 / Rsym value: 0.048 / Net I/av σ(I): 7.59 / Net I/σ(I): 12.2 / Num. measured all: 613035 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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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: 1.2→20 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.976 / WRfactor Rfree: 0.1687 / WRfactor Rwork: 0.1296 / FOM work R set: 0.8715 / SU B: 1.225 / SU ML: 0.025 / SU R Cruickshank DPI: 0.0364 / SU Rfree: 0.0391 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.036 / ESU R Free: 0.039 / 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: 125.32 Å2 / Biso mean: 17.175 Å2 / Biso min: 6.19 Å2
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Refinement step | Cycle: final / Resolution: 1.2→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 14310 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05
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LS refinement shell | Resolution: 1.2→1.231 Å / Total num. of bins used: 20
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