+Open data
-Basic information
Entry | Database: PDB / ID: 5kzt | ||||||
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Title | Listeria monocytogenes OppA bound to peptide | ||||||
Components |
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Keywords | PEPTIDE BINDING PROTEIN / substrate binding protein / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | Function and homology information ATP-binding cassette (ABC) transporter complex / transmembrane transport Similarity search - Function | ||||||
Biological species | Listeria monocytogenes serotype 1/2a Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Light, S.H. / Whiteley, A.T. / Minasov, G. / Portnoy, D.A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To Be Published Title: Listeria monocytogenes OppA bound to peptide Authors: Light, S.H. / Whiteley, A.T. / Minasov, G. / Portnoy, D.A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kzt.cif.gz | 429.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kzt.ent.gz | 351.2 KB | Display | PDB format |
PDBx/mmJSON format | 5kzt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5kzt_validation.pdf.gz | 440.5 KB | Display | wwPDB validaton report |
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Full document | 5kzt_full_validation.pdf.gz | 441.2 KB | Display | |
Data in XML | 5kzt_validation.xml.gz | 46.2 KB | Display | |
Data in CIF | 5kzt_validation.cif.gz | 71.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kz/5kzt ftp://data.pdbj.org/pub/pdb/validation_reports/kz/5kzt | HTTPS FTP |
-Related structure data
Related structure data | 4fajS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 60697.156 Da / Num. of mol.: 2 / Fragment: UNP residues 32-558 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes serotype 1/2a (strain 10403S) (bacteria) Strain: 10403S / Gene: LMRG_01636 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H3GJB6 #2: Protein/peptide | | Mass: 622.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) #3: Protein/peptide | | Mass: 580.502 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) #4: Water | ChemComp-HOH / | |
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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: 2.23 Å3/Da / Density % sol: 44.9 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, sitting drop Details: Protein solution: 12.0 mg/ml, 0.01 M Tris-HCl pH 8.3, and 10/mg/ml tryptone Crystallization condition: Classics II (Qiagen) D10: 0.1 M Bis-Tris pH 6.5 and 20% (w/v) PEG 5000 MME |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.978 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 16, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→30 Å / Num. obs: 92580 / % possible obs: 98.4 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 1.85→1.88 Å / Redundancy: 3 % / Rmerge(I) obs: 0.618 / Mean I/σ(I) obs: 2.3 / CC1/2: 0.58 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4FAJ Resolution: 1.85→30 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.714 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.126 / 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: 21.565 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→30 Å
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Refine LS restraints |
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