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Yorodumi- PDB-7zck: Room temperature crystal structure of PhnD from Synechococcus MIT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zck | |||||||||
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Title | Room temperature crystal structure of PhnD from Synechococcus MITS9220 in complex with phosphate | |||||||||
Components | Phosphonate ABC type transporter/ substrate binding component | |||||||||
Keywords | TRANSPORT PROTEIN / Substrate-binding protein / marine cyanobacteria / urea-binding protein | |||||||||
Function / homology | Putative ABC transporter periplasmic binding protein PhnD-like / Phosphate/phosphite/phosphonate ABC transporter, periplasmic binding protein / ATP-binding cassette (ABC) transporter complex / transmembrane transport / PHOSPHATE ION / Phosphonate ABC type transporter/ substrate binding component Function and homology information | |||||||||
Biological species | Synechococcus sp. MIT S9220 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Mikolajek, H. / Shah, B.S. / Paulsen, I.T. / Sandy, J. / Sanchez-Weatherby, J. | |||||||||
Funding support | Australia, 2items
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Citation | Journal: Iucrj / Year: 2023 Title: Protein-to-structure pipeline for ambient-temperature in situ crystallography at VMXi. Authors: Mikolajek, H. / Sanchez-Weatherby, J. / Sandy, J. / Gildea, R.J. / Campeotto, I. / Cheruvara, H. / Clarke, J.D. / Foster, T. / Fujii, S. / Paulsen, I.T. / Shah, B.S. / Hough, M.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zck.cif.gz | 71.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zck.ent.gz | 50.9 KB | Display | PDB format |
PDBx/mmJSON format | 7zck.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zck_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 7zck_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 7zck_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | 7zck_validation.cif.gz | 18.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zc/7zck ftp://data.pdbj.org/pub/pdb/validation_reports/zc/7zck | HTTPS FTP |
-Related structure data
Related structure data | 8a9dC 8ar6C 8ar9C 8brkC 8brlC 8cifC 7s6gS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 30153.262 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechococcus sp. MIT S9220 (bacteria) / Gene: SynMITS9220_01173 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Lemo21 / References: UniProt: A0A7G8IVX7 | ||||
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#2: Chemical | ChemComp-PO4 / | ||||
#3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-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: 47.42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M Tris pH 8.5, 25 % PEG 3350 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: VMXi / Wavelength: 0.979 Å |
Detector | Type: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: Dec 2, 2020 |
Radiation | Monochromator: Multilayer monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→53.17 Å / Num. obs: 26032 / % possible obs: 99.78 % / Redundancy: 8.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.116 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 1.8→1.82 Å / Redundancy: 5.5 % / Rmerge(I) obs: 1.387 / Mean I/σ(I) obs: 1 / Num. unique obs: 1271 / CC1/2: 0.416 / % possible all: 97.02 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7S6G Resolution: 1.8→53.17 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.962 / SU B: 3.076 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.11 / 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: 31.661 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→53.17 Å
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Refine LS restraints |
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