+Open data
-Basic information
Entry | Database: PDB / ID: 7z00 | ||||||
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Title | Crystal structure of Vibrio alkaline phosphatase in 1.0 M KBr | ||||||
Components | Alkaline phosphatase | ||||||
Keywords | HYDROLASE / Alkaline phosphatase / AP | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Vibrio sp. G15-21 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Markusson, S. / Hjorleifsson, J.G. / Kursula, P. / Asgeirsson, B. | ||||||
Funding support | Iceland, 1items
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Citation | Journal: Biochemistry / Year: 2022 Title: Structural Characterization of Functionally Important Chloride Binding Sites in the Marine Vibrio Alkaline Phosphatase. Authors: Markusson, S. / Hjorleifsson, J.G. / Kursula, P. / Asgeirsson, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7z00.cif.gz | 227.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7z00.ent.gz | 154.5 KB | Display | PDB format |
PDBx/mmJSON format | 7z00.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z0/7z00 ftp://data.pdbj.org/pub/pdb/validation_reports/z0/7z00 | HTTPS FTP |
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-Related structure data
Related structure data | 7qowC 7qp8C 7yzzC 3e2dS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules B
#1: Protein | Mass: 58616.484 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio sp. G15-21 (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): LEMO21 / References: UniProt: Q93P54 |
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-Non-polymers , 5 types, 9 molecules
#2: Chemical | #3: Chemical | ChemComp-BR / | #4: Chemical | #5: Chemical | ChemComp-PO4 / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.19 Å3/Da / Density % sol: 43.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 13.4 mg/mL protein in 24% PEG3350, 1.0 M KBr and 0.1 M Tris pH 7.0. Grown from seed crystals grown in 24% PEG3350, 0.4 M KBr, pH 7.0. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.918 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 9, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→48.39 Å / Num. obs: 209590 / % possible obs: 99.8 % / Redundancy: 7.12 % / Biso Wilson estimate: 71.52 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.156 / Net I/σ(I): 7.96 |
Reflection shell | Resolution: 2.6→2.67 Å / Redundancy: 7.21 % / Num. unique obs: 15872 / CC1/2: 0.371 / Rrim(I) all: 2.994 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3E2D Resolution: 2.6→48.39 Å / SU ML: 0.447 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.7888 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 80.23 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→48.39 Å
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Refine LS restraints |
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LS refinement shell |
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