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Yorodumi- PDB-4km3: Discovery of a novel structural motif in methionine aminopeptidas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4km3 | ||||||
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Title | Discovery of a novel structural motif in methionine aminopeptidase from Streptococci with possible post-translational modification | ||||||
Components | Methionine aminopeptidaseMethionyl aminopeptidase | ||||||
Keywords | HYDROLASE / Classification | ||||||
Function / homology | Function and homology information : / methionyl aminopeptidase / metalloaminopeptidase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Streptococcus pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Arya, T. / Addlagatta, A. | ||||||
Citation | Journal: Plos One / Year: 2013 Title: Discovery of a new genetic variant of methionine aminopeptidase from streptococci with possible post-translational modifications: biochemical and structural characterization. Authors: Arya, T. / Kishor, C. / Saddanapu, V. / Reddi, R. / Addlagatta, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4km3.cif.gz | 118.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4km3.ent.gz | 93.9 KB | Display | PDB format |
PDBx/mmJSON format | 4km3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/km/4km3 ftp://data.pdbj.org/pub/pdb/validation_reports/km/4km3 | HTTPS FTP |
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-Related structure data
Related structure data | 3tb5S S: Starting model for refinement |
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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
#1: Protein | Mass: 31699.051 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: CGSP14 / Gene: map, SPCG_1194 / Production host: Escherichia coli (E. coli) / References: UniProt: B2IQ22 #2: 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: 4.5 Å3/Da / Density % sol: 72.69 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: 0.056 M Sodium phosphate monobasic monohydrate, 1.344M Potassium phosphate dibasic , pH 8.2, 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 | |||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 3, 2013 | |||||||||||||||
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 3.2→23.75 Å / Num. obs: 18507 / % possible obs: 91.64 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rsym value: 0.09 / Net I/σ(I): 14.7 | |||||||||||||||
Reflection shell | Resolution: 3.2→3.26 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 2.493 / Rsym value: 0.7 / % possible all: 91.64 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3TB5 Resolution: 3.2→23.75 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.815 / SU B: 22.316 / SU ML: 0.386 / Cross valid method: THROUGHOUT / ESU R Free: 0.498 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 47.278 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→23.75 Å
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Refine LS restraints |
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