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Yorodumi- PDB-7kz8: Crystal structure of substrate-binding protein Aapf from Pseudomo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7kz8 | |||||||||
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Title | Crystal structure of substrate-binding protein Aapf from Pseudomonas sp. PDC86 | |||||||||
Components | Peptide/nickel transport system substrate-binding protein AapF | |||||||||
Keywords | TRANSPORT PROTEIN / substrate-binding protein (SBPs) / ABC-transporter / type-C SBPs | |||||||||
Function / homology | Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / ATP-binding cassette (ABC) transporter complex / transmembrane transport / Peptide/nickel transport system substrate-binding protein Function and homology information | |||||||||
Biological species | Pseudomonas sp. PDC86 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Luo, S. / Dadhwal, P. / Tong, L. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2021 Title: Structural basis for a bacterial Pip system plant effector recognition protein. Authors: Luo, S. / Coutinho, B.G. / Dadhwal, P. / Oda, Y. / Ren, J. / Schaefer, A.L. / Greenberg, E.P. / Harwood, C.S. / Tong, L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7kz8.cif.gz | 111.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kz8.ent.gz | 82.5 KB | Display | PDB format |
PDBx/mmJSON format | 7kz8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7kz8_validation.pdf.gz | 440.6 KB | Display | wwPDB validaton report |
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Full document | 7kz8_full_validation.pdf.gz | 448.4 KB | Display | |
Data in XML | 7kz8_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | 7kz8_validation.cif.gz | 28.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kz/7kz8 ftp://data.pdbj.org/pub/pdb/validation_reports/kz/7kz8 | HTTPS FTP |
-Related structure data
Related structure data | 7kz9C 1uqwS 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
#1: Protein | Mass: 55089.922 Da / Num. of mol.: 1 / Fragment: substrate-binding proteins, SBPs Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas sp. PDC86 (bacteria) / Gene: AapF / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: A0A1H3V8R8 | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.52 % |
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Crystal grow | Temperature: 298 K / Method: evaporation / pH: 6.5 Details: 0.1 M Bis-Tris (pH 6.5), and 2.6 M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9794 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 8, 2018 / Details: Dectris Eiger 9M | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→47.53 Å / Num. obs: 23962 / % possible obs: 98.1 % / Redundancy: 4.049 % / Biso Wilson estimate: 41.78 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.15 / Rrim(I) all: 0.173 / Χ2: 0.966 / Net I/σ(I): 6.93 / Num. measured all: 97033 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1uqw Resolution: 2.2→47.53 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 29.52 / Stereochemistry target values: ML
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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 max: 85.82 Å2 / Biso mean: 40.4541 Å2 / Biso min: 18.07 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→47.53 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9
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