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Yorodumi- PDB-4wu3: Structure of the PTP-like myo-inositol phosphatase from Mitsuokel... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wu3 | |||||||||
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Title | Structure of the PTP-like myo-inositol phosphatase from Mitsuokella multacida in complex with myo-inositol-(1,3,4,5)-tetrakisphosphate | |||||||||
Components | MYO-INOSITOL PHOSPHOHYDROLASE | |||||||||
Keywords | HYDROLASE | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Mitsuokella multacida (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Bruder, L.M. / Mosimann, S.C. | |||||||||
Funding support | Canada, 2items
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Citation | Journal: To Be Published Title: Structure of the PTP-like phytase from Selenomonas ruminantium in complex with myo-inositol-(1,3,4,5)-tetrakisphosphate Authors: Bruder, L.M. #1: Journal: J. Mol. Biol. / Year: 2009 Title: Structural analysis of a multifunctional, tandemly repeated inositol polyphosphatase. Authors: Gruninger, R.J. / Selinger, L.B. / Mosimann, S.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wu3.cif.gz | 535.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wu3.ent.gz | 436.5 KB | Display | PDB format |
PDBx/mmJSON format | 4wu3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wu/4wu3 ftp://data.pdbj.org/pub/pdb/validation_reports/wu/4wu3 | HTTPS FTP |
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-Related structure data
Related structure data | 4wtyC 3f41S 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 1 / Auth seq-ID: 47 - 636 / Label seq-ID: 39 - 628
NCS ensembles :
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-Components
#1: Protein | Mass: 72448.023 Da / Num. of mol.: 4 / Fragment: UNP residues 32-640 / Mutation: C250S, C548S Source method: isolated from a genetically manipulated source Details: Inactive with C252S/C548S mutations / Source: (gene. exp.) Mitsuokella multacida (bacteria) / Gene: phyA / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A3QMF6, 3-phytase #2: Chemical | ChemComp-4IP / #3: Chemical | ChemComp-PO4 / #4: Chemical | ChemComp-GOL / #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: 2.62 Å3/Da / Density % sol: 53.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: PEG 8000, Polyethylene glycol, Tris chloride, beta-mercapto ethanol, glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97934 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Feb 4, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→44.54 Å / Num. obs: 146418 / % possible obs: 98.8 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 6 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 4.3 / % possible all: 96.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3F41 Resolution: 2.2→44.54 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.906 / SU B: 6.052 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.26 / ESU R Free: 0.184 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.523 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→44.54 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Number: 5556 / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT THERMAL / Weight position: 0.87
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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