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Yorodumi- PDB-6rxg: Crystal Structure of Bifidobacterium longum Multiple Inositol Pol... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rxg | ||||||
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Title | Crystal Structure of Bifidobacterium longum Multiple Inositol Polyphosphate Phosphatase Complex with Phosphate | ||||||
Components | (Histidine acid phosphatase) x 2 | ||||||
Keywords | HYDROLASE / phytase / histidine phosphatase / MINPP / Bifidobacterium | ||||||
Function / homology | inositol phosphate phosphatase activity / Histidine phosphatase superfamily, clade-2 / Histidine phosphatase superfamily (branch 2) / acid phosphatase activity / Histidine phosphatase superfamily / membrane / metal ion binding / PHOSPHATE ION / Histidine acid phosphatase Function and homology information | ||||||
Biological species | Bifidobacterium longum subsp. infantis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å | ||||||
Authors | Zietek, M.A.Z. / Brearley, C.A. / Hemmings, A.M. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2020 Title: Snapshots during the catalytic cycle of a histidine acid phytase reveal an induced-fit structural mechanism. Authors: Acquistapace, I.M. / Zi Etek, M.A. / Li, A.W.H. / Salmon, M. / Kuhn, I. / Bedford, M.R. / Brearley, C.A. / Hemmings, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rxg.cif.gz | 573.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rxg.ent.gz | 474.8 KB | Display | PDB format |
PDBx/mmJSON format | 6rxg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rx/6rxg ftp://data.pdbj.org/pub/pdb/validation_reports/rx/6rxg | HTTPS FTP |
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-Related structure data
Related structure data | 6rxdSC 6rxeC 6rxfC 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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-Components
#1: Protein | Mass: 56494.695 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bifidobacterium longum subsp. infantis (strain ATCC 15697 / DSM 20088 / JCM 1222 / NCTC 11817 / S12) (bacteria) Strain: ATCC 15697 / DSM 20088 / JCM 1222 / NCTC 11817 / S12 Gene: Blon_0263 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Variant (production host): Rosetta 2 (DE3) pLysS / References: UniProt: B7GTV0 | ||||
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#2: Protein | Mass: 56573.672 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bifidobacterium longum subsp. infantis (strain ATCC 15697 / DSM 20088 / JCM 1222 / NCTC 11817 / S12) (bacteria) Strain: ATCC 15697 / DSM 20088 / JCM 1222 / NCTC 11817 / S12 Gene: Blon_0263 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Variant (production host): Rosetta 2 (DE3) pLysS / References: UniProt: B7GTV0 | ||||
#3: Chemical | #4: Chemical | ChemComp-ZN / #5: 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: 2.74 Å3/Da / Density % sol: 55.11 % / Description: needle |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES, 0.01 M zinc chloride, 18 % PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 13, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.71→68.231 Å / Num. obs: 123847 / % possible obs: 95.5 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 7 |
Reflection shell | Resolution: 1.71→1.74 Å / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 6108 / % possible all: 95.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6RXD Resolution: 1.71→68.231 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 18.97
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.71→68.231 Å
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Refine LS restraints |
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LS refinement shell |
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