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- PDB-1b65: Structure of l-aminopeptidase d-ala-esterase/amidase from ochroba... -
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Open data
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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 | ||||||
![]() | PROTEIN (AMINOPEPTIDASE) | ||||||
![]() | HYDROLASE / PEPTIDE DEGRADATION / NTN HYDROLASE | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bompard-Gilles, C. / Villeret, V. / Davies, G.J. / Fanuel, L. / Joris, B. / Frere, J.M. / Van Beeumen, J. | ||||||
![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 430.9 KB | Display | ![]() |
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PDB format | ![]() | 352.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 397.7 KB | Display | ![]() |
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Full document | ![]() | 461.4 KB | Display | |
Data in XML | ![]() | 48.3 KB | Display | |
Data in CIF | ![]() | 76.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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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.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]()
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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 |