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- PDB-4wmf: Crystal structure of catalytically inactive MERS-CoV 3CL protease... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4wmf | |||||||||
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Title | Crystal structure of catalytically inactive MERS-CoV 3CL protease (C148A) in spacegroup P212121 | |||||||||
![]() | MERS-CoV 3CL protease | |||||||||
![]() | HYDROLASE / MES / 3CL protease / coronavirus | |||||||||
Function / homology | ![]() host cell membrane / viral genome replication / methyltransferase activity / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / methylation / cysteine-type deubiquitinase activity ...host cell membrane / viral genome replication / methyltransferase activity / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / methylation / cysteine-type deubiquitinase activity / single-stranded RNA binding / host cell perinuclear region of cytoplasm / viral protein processing / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / cysteine-type endopeptidase activity / virus-mediated perturbation of host defense response / proteolysis / zinc ion binding / membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Lountos, G.T. / Needle, D. / Waugh, D.S. | |||||||||
![]() | ![]() Title: Structures of the Middle East respiratory syndrome coronavirus 3C-like protease reveal insights into substrate specificity. Authors: Needle, D. / Lountos, G.T. / Waugh, D.S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 208.1 KB | Display | ![]() |
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PDB format | ![]() | 165.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4wmdC ![]() 4wmeC ![]() 2ynaS C: citing same article ( 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: 33322.109 Da / Num. of mol.: 3 / Mutation: C148A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: pDN2551 / Production host: ![]() ![]() #2: Chemical | ChemComp-PEG / #3: Chemical | ChemComp-PG4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.93 Å3/Da / Density % sol: 68.7 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20.3 mg/mL protein, well solution: 0,1M Hepes pH 7.5, 0.2M proline, 10% w/v polyethylene glycol 3350 PH range: 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 22, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→50 Å / Num. obs: 107729 / % possible obs: 96.4 % / Redundancy: 7 % / Rsym value: 0.047 / Net I/σ(I): 40.5 |
Reflection shell | Resolution: 1.97→2.02 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.775 / Mean I/σ(I) obs: 2.2 / % possible all: 93.1 |
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Processing
Software | Name: REFMAC / Version: 5.5.0104 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: 2YNA, chain A Resolution: 1.97→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.995 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 28.459 Å2
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Refinement step | Cycle: 1 / Resolution: 1.97→50 Å
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Refine LS restraints |
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