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Yorodumi- PDB-1c23: E. COLI METHIONINE AMINOPEPTIDASE: METHIONINE PHOSPHONATE COMPLEX -
+Open data
-Basic information
Entry | Database: PDB / ID: 1c23 | ||||||
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Title | E. COLI METHIONINE AMINOPEPTIDASE: METHIONINE PHOSPHONATE COMPLEX | ||||||
Components | METHIONINE AMINOPEPTIDASEMethionyl aminopeptidase | ||||||
Keywords | HYDROLASE / PRODUCT COMPLEX | ||||||
Function / homology | Function and homology information : / initiator methionyl aminopeptidase activity / methionyl aminopeptidase / metalloaminopeptidase activity / ferrous iron binding / proteolysis / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||
Authors | Lowther, W.T. / Zhang, Y. / Sampson, P.B. / Honek, J.F. / Matthews, B.W. | ||||||
Citation | Journal: Biochemistry / Year: 1999 Title: Insights into the mechanism of Escherichia coli methionine aminopeptidase from the structural analysis of reaction products and phosphorus-based transition-state analogues. Authors: Lowther, W.T. / Zhang, Y. / Sampson, P.B. / Honek, J.F. / 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 | 1c23.cif.gz | 66.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c23.ent.gz | 47.5 KB | Display | PDB format |
PDBx/mmJSON format | 1c23.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c2/1c23 ftp://data.pdbj.org/pub/pdb/validation_reports/c2/1c23 | 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: 29210.580 Da / Num. of mol.: 1 / Mutation: R175Q Source method: isolated from a genetically manipulated source Details: METHIONINE PHOSPHONATE COMPLEX / Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET28B / Production host: Escherichia coli (E. coli) References: UniProt: P07906, UniProt: P0AE18*PLUS, methionyl aminopeptidase | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-MPH / ( | #5: Water | ChemComp-HOH / | Sequence details | THERE ARE FOUR ADDITIONAL RESIDUES ON THE C-TERMINUS LEFT OVER FROM A THROMBIN DIGEST OF THE HIS- ...THERE ARE FOUR ADDITIONAL | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.36 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: Hepes, NaCl, K2SO4, CoCl2, PEG 4000, methionine, N-octanoyl sucrose, VAPOR DIFFUSION, SITTING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jan 27, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2→32.2 Å / Num. all: 16137 / Num. obs: 79515 / % possible obs: 99.8 % / Redundancy: 4.9 % / Biso Wilson estimate: 15.5 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 27.4 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 6.4 / % possible all: 100 |
Reflection | *PLUS Num. obs: 16137 / Num. measured all: 79515 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.2 |
-Processing
Software |
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Refinement | Resolution: 2→32.2 Å / Stereochemistry target values: TNT /
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Solvent computation | Solvent model: TNT / Bsol: 256.5 Å2 / ksol: 0.839 e/Å3 | |||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→32.2 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | |||||||||||||||
Refinement | *PLUS | |||||||||||||||
Solvent computation | *PLUS | |||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||
Refine LS restraints | *PLUS
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