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Yorodumi- PDB-4ol4: Crystal structure of secreted proline rich antigen MTC28 (Rv0040c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ol4 | ||||||
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Title | Crystal structure of secreted proline rich antigen MTC28 (Rv0040c) from Mycobacterium tuberculosis | ||||||
Components | Proline-rich 28 kDa antigen | ||||||
Keywords | LIPID BINDING PROTEIN / Probable lipoprotein LpqN | ||||||
Function / homology | Lipoprotein LpqN/LpqT-like / Probable lipoprotein LpqN / extracellular region / Proline-rich 28 kDa antigen / Proline-rich 28 kDa antigen Function and homology information | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MIR / MIRAS / Resolution: 2.8 Å | ||||||
Authors | Kundu, P. / Biswas, R. / Mukherjee, S. / Reinhard, L. / Mueller-dieckmann, J. / Weiss, M.S. / Das, A.K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2016 Title: Structure-based Epitope Mapping of Mycobacterium tuberculosis Secretary Antigen MTC28 Authors: Kundu, P. / Biswas, R. / Mukherjee, S. / Reinhard, L. / Dutta, A. / Mueller-Dieckmann, J. / Weiss, M.S. / Pal, N.K. / Das, A.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ol4.cif.gz | 49.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ol4.ent.gz | 34 KB | Display | PDB format |
PDBx/mmJSON format | 4ol4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ol/4ol4 ftp://data.pdbj.org/pub/pdb/validation_reports/ol/4ol4 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29899.729 Da / Num. of mol.: 1 / Fragment: UNP residues 32-310 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: MT0046, mtc28, MTCY21D4.03c, Rv0040c / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: P0A5Q6, UniProt: P9WIM9*PLUS |
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#2: 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: 3.47 Å3/Da / Density % sol: 64.51 % / Mosaicity: 0.19 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 0.2M TMND, 0.1M Bis-tris Propane pH 9.0, 20% PEG MME 2000, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 3, 2013 / Details: mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: VARIMAX (OSMIC MIRROR) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.7→88.521 Å / Num. all: 11663 / Num. obs: 11663 / % possible obs: 99.7 % / Redundancy: 6.8 % / Rsym value: 0.094 / Net I/σ(I): 22.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Phasing
Phasing | Method: MIRAS |
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-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.8→19.48 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.919 / WRfactor Rfree: 0.1817 / WRfactor Rwork: 0.1464 / FOM work R set: 0.8525 / SU B: 8.639 / SU ML: 0.171 / SU R Cruickshank DPI: 0.2853 / SU Rfree: 0.2366 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.285 / ESU R Free: 0.237 / 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: 105.36 Å2 / Biso mean: 42.451 Å2 / Biso min: 19.92 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→19.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.878 Å / Total num. of bins used: 20
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