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Yorodumi- PDB-1b65: Structure of l-aminopeptidase d-ala-esterase/amidase from ochroba... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1b65 | ||||||
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Title | Structure of l-aminopeptidase d-ala-esterase/amidase from ochrobactrum anthropi, a prototype for the serine aminopeptidases, reveals a new variant among the ntn hydrolase fold | ||||||
Components | PROTEIN (AMINOPEPTIDASE) | ||||||
Keywords | HYDROLASE / PEPTIDE DEGRADATION / NTN HYDROLASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Ochrobactrum anthropi (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.82 Å | ||||||
Authors | Bompard-Gilles, C. / Villeret, V. / Davies, G.J. / Fanuel, L. / Joris, B. / Frere, J.M. / Van Beeumen, J. | ||||||
Citation | Journal: Structure Fold.Des. / Year: 2000 Title: A new variant of the Ntn hydrolase fold revealed by the crystal structure of L-aminopeptidase D-ala-esterase/amidase from Ochrobactrum anthropi. Authors: Bompard-Gilles, C. / Villeret, V. / Davies, G.J. / Fanuel, L. / Joris, B. / Frere, J.M. / Van Beeumen, J. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: Crystallization and preliminary X-ray analysis of a new L-aminopeptidase-D-amidase/D-esterase activated by a Gly-Ser peptide bond hydrolysis. Authors: Bompard-Gilles, C. / Villeret, V. / Fanuel, L. / Joris, B. / Frere, J.M. / Van Beeumen, J. #2: Journal: To be Published Title: Structure of L-Aminopeptidase D-Ala-Esterase/ Amidase from Ochrobactrum Anthropi, a Prototype for the Serine Aminopeptidases,Reveals a New Variant Among the Ntn Hydrolase Fold Authors: Bompard-Gilles, C. / Villeret, V. / Davies, G.J. / Fanuel, L. / Joris, B. / Frere, J.M. / Van Beeumen, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1b65.cif.gz | 430.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b65.ent.gz | 352.6 KB | Display | PDB format |
PDBx/mmJSON format | 1b65.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1b65_validation.pdf.gz | 397.7 KB | Display | wwPDB validaton report |
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Full document | 1b65_full_validation.pdf.gz | 461.4 KB | Display | |
Data in XML | 1b65_validation.xml.gz | 48.3 KB | Display | |
Data in CIF | 1b65_validation.cif.gz | 76.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b6/1b65 ftp://data.pdbj.org/pub/pdb/validation_reports/b6/1b65 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 40457.516 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ochrobactrum anthropi (bacteria) / Strain: LMG7991 / Production host: Escherichia coli (E. coli) / References: UniProt: Q59632 #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: 2.43 Å3/Da / Density % sol: 49 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 9 / Details: pH 9.0 | ||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 49 % | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 294 K / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 294 K |
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Diffraction source | Source: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.9 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→12.5 Å / Num. obs: 56600 / % possible obs: 95.8 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rsym value: 0.058 |
Reflection | *PLUS Num. measured all: 473750 / Rmerge(I) obs: 0.081 |
Reflection shell | *PLUS Highest resolution: 1.82 Å / Lowest resolution: 1.9 Å / % possible obs: 91.9 % / Rmerge(I) obs: 0.288 / Mean I/σ(I) obs: 6.9 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.82→12.5 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 1.82→12.5 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / Rfactor obs: 0.169 / Num. reflection obs: 180391 / Num. reflection Rfree: 9535 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |