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Yorodumi- PDB-1ve6: Crystal structure of an acylpeptide hydrolase/esterase from Aerop... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ve6 | ||||||
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Title | Crystal structure of an acylpeptide hydrolase/esterase from Aeropyrum pernix K1 | ||||||
Components | Acylamino-acid-releasing enzymeAcylaminoacyl-peptidase | ||||||
Keywords | HYDROLASE / beta propeller domain / alpha/beta hydrolase domain | ||||||
Function / homology | Function and homology information acylaminoacyl-peptidase / serine-type peptidase activity / omega peptidase activity / proteolysis / cytoplasm Similarity search - Function | ||||||
Biological species | Aeropyrum pernix (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å | ||||||
Authors | Bartlam, M. / Wang, G. / Gao, R. / Yang, H. / Zhao, X. / Xie, G. / Cao, S. / Feng, Y. / Rao, Z. | ||||||
Citation | Journal: STRUCTURE / Year: 2004 Title: Crystal structure of an acylpeptide hydrolase/esterase from Aeropyrum pernix K1 Authors: Bartlam, M. / Wang, G. / Yang, H. / Gao, R. / Zhao, X. / Xie, G. / Cao, S. / Feng, Y. / Rao, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ve6.cif.gz | 236.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ve6.ent.gz | 187.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ve6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ve/1ve6 ftp://data.pdbj.org/pub/pdb/validation_reports/ve/1ve6 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 63108.551 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aeropyrum pernix (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9YBQ2, acylaminoacyl-peptidase #2: Sugar | #3: Chemical | #4: 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: 2.3 Å3/Da / Density % sol: 46.42 % / Description: the file contains Friedel pairs |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG 4000, NaAC, DTT, EDTA, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9795, 0.9799, 0.9800 | ||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 30, 2003 / Details: mirrors | ||||||||||||
Radiation | Monochromator: double-crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.1→50 Å / Num. obs: 118700 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 16.6 | ||||||||||||
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 6.1 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.1→29.77 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: the file contains Friedel pairs
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→29.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.008
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