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Yorodumi- PDB-3o9p: The structure of the Escherichia coli murein tripeptide binding p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3o9p | ||||||
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Title | The structure of the Escherichia coli murein tripeptide binding protein MppA | ||||||
Components | Periplasmic murein peptide-binding protein | ||||||
Keywords | PEPTIDE BINDING PROTEIN/PEPTIDE / oligopeptide binding proteins / murein tripeptide / periplasmic protein / PEPTIDE BINDING PROTEIN-PEPTIDE complex | ||||||
Function / homology | Function and homology information tripeptide transport / oligopeptide binding / tripeptide import across plasma membrane / dipeptide transport / heme transmembrane transport / peptide transport / peptide transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / protein transport / outer membrane-bounded periplasmic space ...tripeptide transport / oligopeptide binding / tripeptide import across plasma membrane / dipeptide transport / heme transmembrane transport / peptide transport / peptide transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / protein transport / outer membrane-bounded periplasmic space / periplasmic space / membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å | ||||||
Authors | Maqbool, A. / Levdikov, V.M. / Blagova, E.V. / Wilkinson, A.J. / Thomas, G.H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Compensating Stereochemical Changes Allow Murein Tripeptide to Be Accommodated in a Conventional Peptide-binding Protein. Authors: Maqbool, A. / Levdikov, V.M. / Blagova, E.V. / Herve, M. / Horler, R.S. / Wilkinson, A.J. / Thomas, G.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3o9p.cif.gz | 123.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3o9p.ent.gz | 93.8 KB | Display | PDB format |
PDBx/mmJSON format | 3o9p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o9/3o9p ftp://data.pdbj.org/pub/pdb/validation_reports/o9/3o9p | HTTPS FTP |
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-Related structure data
Related structure data | 2z23S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 58036.570 Da / Num. of mol.: 1 / Fragment: UNP residues 23-537 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: b1329, JW1322, mppA, ynaH / Plasmid: pET-YSBLIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P77348 | ||
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#2: Chemical | ChemComp-MHI / | ||
#3: Chemical | ChemComp-ZN / #4: 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: 2.59 Å3/Da / Density % sol: 52.45 % |
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Crystal grow | Temperature: 293 K / pH: 6.5 Details: 20% PEG3350, 50mM zinc acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.935 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 11, 2009 / Details: TOROIDAL FOCUSING MIRROR |
Radiation | Monochromator: SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.935 Å / Relative weight: 1 |
Reflection | Resolution: 2.06→50 Å / Num. obs: 34597 / % possible obs: 92 % / Observed criterion σ(I): 0 / Redundancy: 9.7 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 20.6 |
Reflection shell | Resolution: 2.06→2.1 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.553 / Mean I/σ(I) obs: 1.6 / % possible all: 33.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2Z23 Resolution: 2.07→41.27 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.385 / SU ML: 0.116 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.195 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 24.863 Å2
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Refinement step | Cycle: LAST / Resolution: 2.07→41.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.073→2.126 Å / Total num. of bins used: 20
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