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Open data
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Basic information
Entry | Database: PDB / ID: 7sci | ||||||
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Title | AM0627 metallopeptidase from Akkermansia muciniphila | ||||||
![]() | Peptidase M60 domain-containing protein | ||||||
![]() | HYDROLASE / Metalloenzyme / O-glycoprotease / mucinase | ||||||
Function / homology | ![]() M60-like domain, N-terminal / N-terminal domain of M60-like peptidases / Peptidase family M60 domain / Peptidase M60, enhancin-like domain 3 / Peptidase M60, enhancin and enhancin-like / Peptidase family M60 domain profile. / Peptidase M60-like family Similarity search - Domain/homology | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Fernandez, D. / Bertozzi, C.R. / Shon, D.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure-guided mutagenesis of a mucin-selective metalloprotease from Akkermansia muciniphila alters substrate preferences. Authors: Shon, D.J. / Fernandez, D. / Riley, N.M. / Ferracane, M.J. / Bertozzi, C.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 123.5 KB | Display | ![]() |
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PDB format | ![]() | 90.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 451.5 KB | Display | ![]() |
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Full document | ![]() | 454.1 KB | Display | |
Data in XML | ![]() | 22.4 KB | Display | |
Data in CIF | ![]() | 33.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5kd5S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 55311.645 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC BAA-835 / DSM 22959 / JCM 33894 / BCRC 81048 / CCUG 64013 / CIP 107961 / Muc Gene: Amuc_0627 / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 359 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / | ||||
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#3: Chemical | ChemComp-PGE / | ||||
#4: Chemical | ChemComp-FMT / #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 60.14 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / Details: PEG 4000, glycerol, HEPES/MOPS, alcohols |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 15, 2020 Details: Flat Si Rh coated M0, Kirkpatrick-Baez flat bent Si M1 & M2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Liquid nitrogen-cooled double crystal, non fixed exit slit Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→87.957 Å / Num. all: 52780 / Num. obs: 52780 / % possible obs: 99.9 % / Redundancy: 4.9 % / Rpim(I) all: 0.052 / Rrim(I) all: 0.118 / Rsym value: 0.105 / Net I/av σ(I): 5.3 / Net I/σ(I): 8.9 / Num. measured all: 258687 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5KD5 Resolution: 1.9→29.96 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.219 / SU ML: 0.09 / SU R Cruickshank DPI: 0.1184 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: 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 / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 100.66 Å2 / Biso mean: 31.165 Å2 / Biso min: 16.04 Å2
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Refinement step | Cycle: final / Resolution: 1.9→29.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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