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Yorodumi- PDB-8a42: Crystal structure of the pneumococcal Substrate-binding protein A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8a42 | ||||||
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Title | Crystal structure of the pneumococcal Substrate-binding protein AmiA in complex with an unknown peptide | ||||||
Components |
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Keywords | PEPTIDE BINDING PROTEIN / Permease / Pneumococcus / AmiA / peptide / substrate-binding protein | ||||||
Function / homology | Function and homology information peptide transport / ATP-binding cassette (ABC) transporter complex / transmembrane transport / protein transport / periplasmic space Similarity search - Function | ||||||
Biological species | Streptococcus pneumoniae (bacteria) Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.5 Å | ||||||
Authors | Alcorlo, M. / Abdullah, M.R. / Hammerschmidt, S. / Hermoso, J. | ||||||
Funding support | Spain, 1items
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Citation | Journal: To Be Published Title: Crystal structure of the pneumococcal Substrate-binding protein AmiA in complex with an unknown peptide Authors: Alcorlo, M. / Abdullah, M.R. / Hammerschmidt, S. / Hermoso, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8a42.cif.gz | 271.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8a42.ent.gz | 214.9 KB | Display | PDB format |
PDBx/mmJSON format | 8a42.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a4/8a42 ftp://data.pdbj.org/pub/pdb/validation_reports/a4/8a42 | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 70394.305 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: ATCC BAA-334 / TIGR4 / Gene: amiA, SP_1891 / Production host: Escherichia coli (E. coli) / References: UniProt: P18791 |
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#2: Protein/peptide | Mass: 869.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) |
#3: 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: 2.2 Å3/Da / Density % sol: 44.03 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 200 mM Amonium Sulfate and 20% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 25, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→47.645 Å / Num. obs: 97923 / % possible obs: 97.2 % / Redundancy: 7.6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.026 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 1.5→1.55 Å / Rmerge(I) obs: 0.549 / Num. unique obs: 4649 / CC1/2: 0.84 / Rpim(I) all: 0.218 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 1.5→47.645 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.36 / 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: 81.49 Å2 / Biso mean: 17.5117 Å2 / Biso min: 5.53 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.5→47.645 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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