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Yorodumi- PDB-3f7m: Crystal structure of apo Cuticle-Degrading Protease (ver112) from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3f7m | ||||||
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Title | Crystal structure of apo Cuticle-Degrading Protease (ver112) from Verticillium psalliotae | ||||||
Components | Alkaline serine protease ver112 | ||||||
Keywords | HYDROLASE / Verticillium psalliotae / Cuticle-Degrading Protease / Nematodes / Protease / Secreted / Serine protease / Zymogen | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type endopeptidase activity / extracellular region Similarity search - Function | ||||||
Biological species | Lecanicillium psalliotae (fungus) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Liang, L. / Lou, Z. / Ye, F. / Meng, Z. / Rao, Z. / Zhang, K. | ||||||
Citation | Journal: Faseb J. / Year: 2010 Title: The crystal structures of two cuticle-degrading proteases from nematophagous fungi and their contribution to infection against nematodes. Authors: Liang, L. / Meng, Z. / Ye, F. / Yang, J. / Liu, S. / Sun, Y. / Guo, Y. / Mi, Q. / Huang, X. / Zou, C. / Rao, Z. / Lou, Z. / Zhang, K.Q. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3f7m.cif.gz | 67 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3f7m.ent.gz | 48.6 KB | Display | PDB format |
PDBx/mmJSON format | 3f7m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3f7m_validation.pdf.gz | 426.3 KB | Display | wwPDB validaton report |
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Full document | 3f7m_full_validation.pdf.gz | 435.7 KB | Display | |
Data in XML | 3f7m_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 3f7m_validation.cif.gz | 22.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f7/3f7m ftp://data.pdbj.org/pub/pdb/validation_reports/f7/3f7m | HTTPS FTP |
-Related structure data
Related structure data | 3f7oC 1bjrS C: citing same article (ref.) S: Starting model for refinement |
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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: 28575.592 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Lecanicillium psalliotae (fungus) References: UniProt: Q68GV9, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.85 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 25% PEG 3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 15, 2007 / Details: osmic mirror |
Radiation | Monochromator: osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 26891 / % possible obs: 99 % / Observed criterion σ(F): 0 / Redundancy: 8 % / Rmerge(I) obs: 0.034 |
Reflection shell | Resolution: 1.6→1.7 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.138 / Num. unique all: 2077 / % possible all: 75.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BJR Resolution: 1.6→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.6→50 Å
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Refine LS restraints |
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