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Yorodumi- PDB-5ypd: Mycobacterium Tuberculosis Methionine aminopeptidase type 1c (C10... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ypd | ||||||
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Title | Mycobacterium Tuberculosis Methionine aminopeptidase type 1c (C105N mutant) in complex with Methionine | ||||||
Components | Methionine aminopeptidaseMethionyl aminopeptidase | ||||||
Keywords | HYDROLASE / Methionine aminopeptidase | ||||||
Function / homology | Function and homology information initiator methionyl aminopeptidase activity / methionyl aminopeptidase / metalloaminopeptidase activity / transition metal ion binding / proteolysis Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.62 Å | ||||||
Authors | Sandeep, C.B. / Addlagatta, A. | ||||||
Funding support | India, 1items
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Citation | Journal: Int.J.Biol.Macromol. / Year: 2019 Title: Discovery of a new class of type 1 methionine aminopeptidases that have relaxed substrate specificity. Authors: Bala, S.C. / Haque, N. / Pillalamarri, V. / Reddi, R. / Kashyap, R. / Marapaka, A.K. / Addlagatta, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ypd.cif.gz | 77.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ypd.ent.gz | 53.8 KB | Display | PDB format |
PDBx/mmJSON format | 5ypd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yp/5ypd ftp://data.pdbj.org/pub/pdb/validation_reports/yp/5ypd | HTTPS FTP |
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-Related structure data
Related structure data | 5ypjC 1yj3S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 34453.730 Da / Num. of mol.: 1 / Mutation: C105N, C284A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra) (bacteria) Strain: ATCC 25177 / H37Ra / Gene: mapB, map, MRA_2886 / Production host: Escherichia coli (E. coli) / References: UniProt: A5U6L5, methionyl aminopeptidase |
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-Non-polymers , 6 types, 167 molecules
#2: Chemical | #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-MET / | #6: Chemical | #7: 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: 1.83 Å3/Da / Density % sol: 32.91 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M Hepes, 27% Peg 3350, 3% Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 1, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.62→28.57 Å / Num. obs: 29506 / % possible obs: 90.7 % / Redundancy: 1.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.044 / Rrim(I) all: 0.062 / Χ2: 1.034 / Net I/av σ(I): 11.69 / Net I/σ(I): 34 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 1.9 %
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1YJ3 Resolution: 1.62→28.57 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.438 / SU ML: 0.051 / SU R Cruickshank DPI: 0.0875 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.09 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 71.63 Å2 / Biso mean: 26.91 Å2 / Biso min: 16.24 Å2
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Refinement step | Cycle: final / Resolution: 1.62→28.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.621→1.663 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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