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Yorodumi- PDB-5isu: 2.2 Angstrom Crystal Structure of ABC Transporter Substrate Bindi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5isu | ||||||
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Title | 2.2 Angstrom Crystal Structure of ABC Transporter Substrate Binding Protein CtaP (Lmo0135) from Listeria monocytogenes. | ||||||
Components | Lmo0135 protein | ||||||
Keywords | TRANSPORT PROTEIN / ABC Transporter / CSGID / Structural Genomics / Center for Structural Genomics of Infectious Diseases | ||||||
Function / homology | Function and homology information peptide transport / peptide transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / outer membrane-bounded periplasmic space Similarity search - Function | ||||||
Biological species | Listeria monocytogenes EGD-e (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Minasov, G. / Light, S.H. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To Be Published Title: 2.2 Angstrom Crystal Structure of ABC Transporter Substrate Binding Protein CtaP (Lmo0135) from Listeria monocytogenes. Authors: Minasov, G. / Light, S.H. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5isu.cif.gz | 213.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5isu.ent.gz | 169.2 KB | Display | PDB format |
PDBx/mmJSON format | 5isu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/is/5isu ftp://data.pdbj.org/pub/pdb/validation_reports/is/5isu | HTTPS FTP |
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-Related structure data
Related structure data | 4oetS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 56142.227 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes EGD-e (bacteria) Strain: ATCC BAA-679 / EGD-e / Gene: lmo0135 / Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-Magic / References: UniProt: Q8YAJ0 |
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#2: Chemical | ChemComp-EDO / |
#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: 2.17 Å3/Da / Density % sol: 43.3 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Protein: 15.0 mg/ml, 0.1M Tris HCl (pH 8.3), 0.5mM Cysteine; Screen: Classics II (D8), 0.1M HEPES (pH 7.5), 25% (w/v) PEG3350. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 25, 2016 / Details: C(111) |
Radiation | Monochromator: beryllium lenses / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→29.1 Å / Num. obs: 24855 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 47.1 Å2 / CC1/2: 0.629 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 24.5 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.756 / Mean I/σ(I) obs: 2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4OET Resolution: 2.2→29.1 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.949 / SU B: 14.073 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.303 / ESU R Free: 0.209 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.746 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→29.1 Å
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Refine LS restraints |
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