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- PDB-6iy4: Crystal structure of a psychrophilic marine protease MP inhibitor -
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Open data
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Basic information
Entry | Database: PDB / ID: 6iy4 | ||||||
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Title | Crystal structure of a psychrophilic marine protease MP inhibitor | ||||||
![]() | LupI | ||||||
![]() | HYDROLASE INHIBITOR / psychrophilic marine protease inhibitor | ||||||
Function / homology | Protease inhibitor / Alkaline proteinase inhibitor/ Outer membrane lipoprotein Omp19 / Protease inhibitor Inh / Protease inhibitor, beta-barrel domain / metalloendopeptidase inhibitor activity / periplasmic space / LupI![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hao, J.H. / Zhang, L.H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of a psychrophilic marine protease MP inhibitor Authors: Hao, J.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 30.8 KB | Display | ![]() |
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PDB format | ![]() | 18.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 420.5 KB | Display | ![]() |
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Full document | ![]() | 420.4 KB | Display | |
Data in XML | ![]() | 5.4 KB | Display | |
Data in CIF | ![]() | 6.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ixxS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 10104.364 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Water | ChemComp-HOH / |
Sequence details | Author states that the sequence G3MEU6 may have errors in sequencing, and this time the sequence is ...Author states that the sequence G3MEU6 may have errors in sequencing, and this time the sequence is re-sequence verified to be Leu. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.57 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 6.5 / Details: 0.1M NaCl, 0.1M BIS-TRIS pH 6.5, 1.5M (NH4)2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 15, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→50 Å / Num. obs: 11707 / % possible obs: 99.7 % / Redundancy: 5.4 % / CC1/2: 0.991 / Rmerge(I) obs: 0.213 / Rpim(I) all: 0.088 / Net I/σ(I): 11 |
Reflection shell | Resolution: 1.59→1.64 Å / Rmerge(I) obs: 0.654 / Num. unique obs: 5628 / CC1/2: 0.869 / Rpim(I) all: 0.277 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6IXX Resolution: 1.59→31.31 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.784 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.09 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 67.91 Å2 / Biso mean: 25.274 Å2 / Biso min: 16.75 Å2
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Refinement step | Cycle: final / Resolution: 1.59→31.31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.586→1.627 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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