+Open data
-Basic information
Entry | Database: PDB / ID: 4kb5 | ||||||
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Title | Crystal structure of MycP1 from Mycobacterium smegmatis | ||||||
Components | Membrane-anchored mycosin mycp1 | ||||||
Keywords | HYDROLASE / subtilisin-like serine protease / subtilase family / catalytic triad / autoinhibition / Serine protease | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type endopeptidase activity / proteolysis / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium smegmatis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å | ||||||
Authors | Sun, D.M. / He, Y. / Tian, C.L. | ||||||
Citation | Journal: Protein Cell / Year: 2013 Title: The putative propeptide of MycP1 in mycobacterial type VII secretion system does not inhibit protease activity but improves protein stability. Authors: Sun, D. / Liu, Q. / He, Y. / Wang, C. / Wu, F. / Tian, C. / Zang, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kb5.cif.gz | 85.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kb5.ent.gz | 67.8 KB | Display | PDB format |
PDBx/mmJSON format | 4kb5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kb/4kb5 ftp://data.pdbj.org/pub/pdb/validation_reports/kb/4kb5 | HTTPS FTP |
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-Related 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: 42502.203 Da / Num. of mol.: 1 / Fragment: UNP residues 24-422 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_0083, MSMEI_0081 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0QNL1 | ||
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#2: Chemical | ChemComp-GOL / #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: 4.12 Å3/Da / Density % sol: 70.11 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 1.6 M Magnesium sulfate, 0.1 M MES pH 5.5 with a protein concentration of 20 mg ml-1, VAPOR DIFFUSION, SITTING DROP, temperature 283K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97914 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 21, 2012 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97914 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→77.89 Å / Num. all: 39312 / Num. obs: 39312 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.6 % / Biso Wilson estimate: 34.6 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 25.9 |
Reflection shell | Resolution: 2.15→2.19 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 4.1 / Num. unique all: 1947 / Rsym value: 0.507 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.15→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.691 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.144 / ESU R Free: 0.134 / 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: 39.261 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.151→2.207 Å / Total num. of bins used: 20
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