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Yorodumi- PDB-1y1n: Identification of SH3 motif in M. Tuberculosis methionine aminope... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1y1n | ||||||
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Title | Identification of SH3 motif in M. Tuberculosis methionine aminopeptidase suggests a mode of interaction with the ribosome | ||||||
Components | Methionine aminopeptidase 1B | ||||||
Keywords | HYDROLASE / Methionine aminopeptidase / MtMetAP1B / PxxP / SH3 / ribosome / L24 | ||||||
Function / homology | Function and homology information : / initiator methionyl aminopeptidase activity / methionyl aminopeptidase / cobalt ion binding / metalloaminopeptidase activity / protein processing / iron ion binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å | ||||||
Authors | Addlagatta, A. / Quillin, M.L. / Omotoso, O. / Liu, J.O. / Matthews, B.W. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Identification of an SH3-Binding Motif in a New Class of Methionine Aminopeptidases from Mycobacterium tuberculosis Suggests a Mode of Interaction with the Ribosome Authors: Addlagatta, A. / Quillin, M.L. / Omotoso, O. / Liu, J.O. / Matthews, B.W. #1: Journal: Chem.Rev. / Year: 2002 Title: Metalloaminopeptidases: Common functional themes in disparate structural surroundings Authors: Lowther, W.T. / Matthews, B.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1y1n.cif.gz | 75.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1y1n.ent.gz | 54.8 KB | Display | PDB format |
PDBx/mmJSON format | 1y1n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1y1n_validation.pdf.gz | 429 KB | Display | wwPDB validaton report |
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Full document | 1y1n_full_validation.pdf.gz | 432.6 KB | Display | |
Data in XML | 1y1n_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | 1y1n_validation.cif.gz | 24.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y1/1y1n ftp://data.pdbj.org/pub/pdb/validation_reports/y1/1y1n | HTTPS FTP |
-Related structure data
Related structure data | 1yj3C 1c21S 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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Details | Biological unit is a monomer as seen in the assyemetric unit |
-Components
#1: Protein | Mass: 31750.783 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) Description: N-terminal His-tag was kept during crystallization but is not visible in the elecron density maps Gene: map, mapB / Plasmid: pET28a MtMetAP1B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P0A5J2, UniProt: P9WK19*PLUS, methionyl aminopeptidase |
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#2: Chemical | ChemComp-K / |
#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: 2.17 Å3/Da / Density % sol: 43.2 % |
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Crystal grow | Temperature: 273 K / Method: vapor diffusion / pH: 6.5 Details: Bistris, PEG monomethyl ether 2000, KCl, HEPES, NaCl, pH 6.5, VAPOR DIFFUSION, temperature 273K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.977 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Monochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 1.51→20 Å / Num. all: 41440 / Num. obs: 41440 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 26 % / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 30.6 |
Reflection shell | Resolution: 1.51→1.56 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.164 / Mean I/σ(I) obs: 7.67 / Num. unique all: 4038 / Rsym value: 0.154 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1C21 Resolution: 1.51→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 21.1 Å2
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Refine analyze | Luzzati coordinate error obs: 0.2 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.25 Å | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.51→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.51→1.56 Å
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