[English] 日本語
Yorodumi- PDB-1agy: The 1.15 angstrom refined structure of fusarium solani pisi cutinase -
+Open data
-Basic information
Entry | Database: PDB / ID: 1agy | ||||||
---|---|---|---|---|---|---|---|
Title | The 1.15 angstrom refined structure of fusarium solani pisi cutinase | ||||||
Components | CUTINASE | ||||||
Keywords | SERINE ESTERASE / HYDROLASE / GLYCOPROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Nectria haematococca mpVI (fungus) | ||||||
Method | X-RAY DIFFRACTION / RESOLUTION EXTENSION / Resolution: 1.15 Å | ||||||
Authors | Nicolas, A. / Martinez, C. / Cambillau, C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1997 Title: Atomic resolution (1.0 A) crystal structure of Fusarium solani cutinase: stereochemical analysis. Authors: Longhi, S. / Czjzek, M. / Lamzin, V. / Nicolas, A. / Cambillau, C. #1: Journal: Nature / Year: 1992 Title: Fusarium Solani Cutinase is a Lipolytic Enzyme with a Catalytic Serine Accessible to Solvent Authors: Martinez, C. / De Geus, P. / Lauwereys, M. / Matthyssens, G. / Cambillau, C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1agy.cif.gz | 105 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1agy.ent.gz | 84 KB | Display | PDB format |
PDBx/mmJSON format | 1agy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1agy_validation.pdf.gz | 415.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1agy_full_validation.pdf.gz | 416.7 KB | Display | |
Data in XML | 1agy_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | 1agy_validation.cif.gz | 19.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/1agy ftp://data.pdbj.org/pub/pdb/validation_reports/ag/1agy | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 20828.400 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nectria haematococca mpVI (fungus) / Species: Nectria haematococca / Strain: mpVI / Production host: Escherichia coli (E. coli) References: UniProt: P00590, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases |
---|---|
#2: Water | ChemComp-HOH / |
Sequence details | REGARDING IDENTITY OF RESIDUE ARG 32, UPON QUESTIONING OF TOMMY CARSTENSEN, AUTHORS SONIA LONGHI ...REGARDING IDENTITY OF RESIDUE ARG 32, UPON QUESTIONIN |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
---|
-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 38 % | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 7 Details: PROTEIN WAS CRYSTALLIZED FROM 15 - 20% PEG 6000, 0.1 M HEPES, PH 7.0 | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop / Details: Abergel, C., (1990) J. Mol. Biol., 215, 215. | ||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 288 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: NICOLET / Detector: AREA DETECTOR / Date: Jan 1, 1993 / Details: NO |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→20 Å / Num. obs: 60972 / % possible obs: 95.22 % / Observed criterion σ(I): 0 / Redundancy: 4.09 % / Biso Wilson estimate: 8.43 Å2 / Rmerge(I) obs: 0.01 / Rsym value: 0.01 / Net I/σ(I): 27.46 |
Reflection shell | Resolution: 1.15→1.2 Å / Redundancy: 2 % / Rmerge(I) obs: 0.03 / Mean I/σ(I) obs: 3.21 / Rsym value: 0.03 / % possible all: 84.2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: RESOLUTION EXTENSION Starting model: CUTINASE STRUCTURE AT 1.6 ANGSTROM RESOLUTION Resolution: 1.15→20 Å / Rfactor Rfree error: 0 / Data cutoff high absF: 1.15 / Data cutoff low absF: 6 / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.54 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati sigma a obs: 0.01 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.15→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.15→1.2 Å / Rfactor Rfree error: 0 / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.4 / Rfactor Rwork: 0.4 |