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Yorodumi- PDB-3o6z: Structure of the D152A E.coli GDP-mannose hydrolase (yffh) in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3o6z | ||||||
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Title | Structure of the D152A E.coli GDP-mannose hydrolase (yffh) in complex with Mg++ | ||||||
Components | GDP-mannose pyrophosphatase nudK | ||||||
Keywords | HYDROLASE / nudix / GDP_mannose / biofilm | ||||||
Function / homology | Function and homology information GDP-mannose hydrolase activity / nucleoside phosphate metabolic process / ribose phosphate metabolic process / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / magnesium ion binding / protein homodimerization activity / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Amzel, L.M. / Gabelli, S.B. / Boto, A.N. | ||||||
Citation | Journal: Proteins / Year: 2011 Title: Structural studies of the Nudix GDP-mannose hydrolase from E. coli reveals a new motif for mannose recognition. Authors: Boto, A.N. / Xu, W. / Jakoncic, J. / Pannuri, A. / Romeo, T. / Bessman, M.J. / Gabelli, S.B. / Amzel, L.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3o6z.cif.gz | 170.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3o6z.ent.gz | 135.3 KB | Display | PDB format |
PDBx/mmJSON format | 3o6z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o6/3o6z ftp://data.pdbj.org/pub/pdb/validation_reports/o6/3o6z | HTTPS FTP |
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-Related structure data
Related structure data | 3o52SC 3o61C 3o69C 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 21729.623 Da / Num. of mol.: 2 / Mutation: D152A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b2467, JW2451, nudK, yffH / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: P37128, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides |
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-Non-polymers , 5 types, 337 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-TRS / | #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: 2.34 Å3/Da / Density % sol: 47.34 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 20-26% PEG 3350, 0.2 M MgCl2, 0.1 M Tris pH 8.5, 4 mM GDP-mannose at a ratio of 1:1 protein:reservoir, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.54 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 30, 2009 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.03→20.47 Å / Num. obs: 26521 / % possible obs: 98 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.077 / Χ2: 2.956 / Net I/σ(I): 16.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3O52 Resolution: 2.05→20.47 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.872 / WRfactor Rfree: 0.2731 / WRfactor Rwork: 0.2147 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7718 / SU B: 9.966 / SU ML: 0.152 / SU R Cruickshank DPI: 0.2777 / SU Rfree: 0.2387 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 80.34 Å2 / Biso mean: 34.263 Å2 / Biso min: 15.63 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→20.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.103 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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