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Yorodumi- PDB-3mat: E.COLI METHIONINE AMINOPEPTIDASE TRANSITION-STATE INHIBITOR COMPLEX -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mat | |||||||||
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Title | E.COLI METHIONINE AMINOPEPTIDASE TRANSITION-STATE INHIBITOR COMPLEX | |||||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / ALPHA-AMINOACYLPEPTIDE / TRANSITION-STATE ANALOG / HYDROLASE-HYDROLASE INHIBITOR 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 / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Lowther, W.T. / Orville, A.M. / Madden, D.T. / Lim, S. / Rich, D.H. / Matthews, B.W. | |||||||||
Citation | Journal: Biochemistry / Year: 1999 Title: Escherichia coli methionine aminopeptidase: implications of crystallographic analyses of the native, mutant, and inhibited enzymes for the mechanism of catalysis. Authors: Lowther, W.T. / Orville, A.M. / Madden, D.T. / Lim, S. / Rich, D.H. / Matthews, B.W. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1998 Title: The anti-angiogenic agent fumagillin covalently modifies a conserved active-site histidine in the Escherichia coli methionine aminopeptidase. Authors: Lowther, W.T. / McMillen, D.A. / Orville, A.M. / Matthews, B.W. #2: Journal: Biochemistry / Year: 1993 Title: Structure of the cobalt-dependent methionine aminopeptidase from Escherichia coli: a new type of proteolytic enzyme. Authors: Roderick, S.L. / 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 | 3mat.cif.gz | 70.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mat.ent.gz | 49.1 KB | Display | PDB format |
PDBx/mmJSON format | 3mat.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ma/3mat ftp://data.pdbj.org/pub/pdb/validation_reports/ma/3mat | HTTPS FTP |
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-Related structure data
Related structure data | 2matSC 4matC 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
#1: Protein | Mass: 29454.932 Da / Num. of mol.: 1 / Mutation: R175Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET28B / Cell line (production host): BL21(DE3) / Production host: Escherichia coli (E. coli) References: UniProt: P07906, UniProt: P0AE18*PLUS, methionyl aminopeptidase | ||||||
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#2: Protein/peptide | Mass: 605.766 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHETIC | ||||||
#3: Chemical | #4: Chemical | ChemComp-NA / | #5: Water | ChemComp-HOH / | Sequence details | GLN 175, SITE-DIRECTED MUTANT THE PROTEIN WAS TREATED WITH THROMBIN THAT LEFT PART OF THE CLEAVAGE ...GLN 175, SITE-DIRECTED MUTANT THE PROTEIN WAS TREATED WITH THROMBIN THAT LEFT PART OF THE CLEAVAGE SITE RECOGNITIO | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.1 Details: CRYSTALS OF THE CO(II)-SUBSTITUTED ENZYME WERE GROWN AT ROOM TEMPERATURE BY VAPOR DIFFUSION IN 20-30 UL SITTING DROPS AFTER MIXING THE PROTEIN, 12 MG/ML SOLUTION IN STORAGE BUFFER(25 MM ...Details: CRYSTALS OF THE CO(II)-SUBSTITUTED ENZYME WERE GROWN AT ROOM TEMPERATURE BY VAPOR DIFFUSION IN 20-30 UL SITTING DROPS AFTER MIXING THE PROTEIN, 12 MG/ML SOLUTION IN STORAGE BUFFER(25 MM HEPES PH 6.8, 25 MM K2SO4, 100 MM NACL, 1 MM COCL2, 15 MM METHIONINE),CONTAINING 48.8 MM N-OCTANOYL SUCROSE, 1:1 WITH WELL SOLUTIONS (24-26% PEG4000, 0.1M HEPES PH7.0-7.2,FRESH 2 MM COCL2). CRYSTALS WERE OBTAINED OF THE INHIBITOR COMPLEX BY INCUBATING THE PROTEIN AS ABOVE AT ROOM TEMPERATURE FOR 5 MIN WITH A 20-FOLD MOLAR EXCESS OF THE INHIBITOR DISSOLVED IN DMSO. THE FINAL INHIBITOR:ENZYME RATIO WAS 10:1 (1% DMSO) AFTER MIXING THE PREFORMED COMPLEX WITH WELL SOLUTION (0.1M MES PH 6.1, | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||
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 RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 21, 1998 |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→37.8 Å / Num. obs: 13762 / % possible obs: 94 % / Redundancy: 3.3 % / Biso Wilson estimate: 17.4 Å2 / Rsym value: 0.076 / Net I/σ(I): 20.5 |
Reflection shell | Resolution: 2.1→2.18 Å / Mean I/σ(I) obs: 4.9 / Rsym value: 0.255 / % possible all: 92.9 |
Reflection | *PLUS % possible obs: 94 % / Num. measured all: 45928 / Rmerge(I) obs: 0.076 |
Reflection shell | *PLUS % possible obs: 92.9 % / Rmerge(I) obs: 0.255 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2MAT Resolution: 2→37.8 Å / Isotropic thermal model: TNT BCORREL V1.0 / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
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Solvent computation | Solvent model: TNT / Bsol: 283.1 Å2 / ksol: 0.898 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→37.8 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5F / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.1 Å / σ(F): 0 / Rfactor all: 0.156 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 17.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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