+Open data
-Basic information
Entry | Database: PDB / ID: 7jls | ||||||
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Title | RV3666c bound to tripeptide | ||||||
Components |
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Keywords | PEPTIDE BINDING PROTEIN / RV3666c Peptide binding protein | ||||||
Function / homology | peptide transport / Peptide/nickel binding protein, MppA-type / peptide transmembrane transporter activity / 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 / outer membrane-bounded periplasmic space / Probable periplasmic dipeptide-binding lipoprotein DppA Function and homology information | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) Escherichia coli BL21 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / MAD / Resolution: 1.52 Å | ||||||
Authors | Lee, R.E. / Griffith, E.C. / Miller, D.J. | ||||||
Funding support | United States, 1items
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Citation | Journal: Tuberculosis (Edinb) / Year: 2021 Title: Biophysical analysis of the Mycobacteria tuberculosis peptide binding protein DppA reveals a stringent peptide binding pocket. Authors: Fernando, D.M. / Gee, C.T. / Griffith, E.C. / Meyer, C.J. / Wilt, L.A. / Tangallapally, R. / Wallace, M.J. / Miller, D.J. / Lee, R.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7jls.cif.gz | 116.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jls.ent.gz | 90.8 KB | Display | PDB format |
PDBx/mmJSON format | 7jls.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jl/7jls ftp://data.pdbj.org/pub/pdb/validation_reports/jl/7jls | HTTPS FTP |
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-Related structure data
Similar structure data |
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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: 60615.273 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: dppA, Rv3666c / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I6X811 |
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#2: Protein/peptide | Mass: 275.302 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria) |
#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: 1.91 Å3/Da / Density % sol: 35.73 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2M ammonium sulfate pH7.0, 18-23% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Oct 27, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.52→61.64 Å / Num. obs: 70699 / % possible obs: 99.4 % / Redundancy: 4 % / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.039 / Rrim(I) all: 0.08 / Χ2: 1.51 / Net I/σ(I): 13.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.52→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.931 / SU B: 1.512 / SU ML: 0.056 / SU R Cruickshank DPI: 0.0872 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 67.64 Å2 / Biso mean: 22.506 Å2 / Biso min: 11.52 Å2
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Refinement step | Cycle: final / Resolution: 1.52→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.514→1.553 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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