+Open data
-Basic information
Entry | Database: PDB / ID: 7yzx | ||||||||||||
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Title | ScpA from Streptococcus pyogenes, D783A mutant. | ||||||||||||
Components | C5a peptidase | ||||||||||||
Keywords | HYDROLASE / C5a peptidase / virulence factor | ||||||||||||
Function / homology | Function and homology information C5a peptidase / serine-type endopeptidase activity / proteolysis / membrane / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Streptococcus pyogenes (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||||||||
Authors | Kagawa, T.F. / Cooney, J.C. / Jain, M. | ||||||||||||
Funding support | Ireland, 3items
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Citation | Journal: Data Brief / Year: 2023 Title: X-ray diffraction data for the C5a-peptidase mutant with modified activity and specificity. Authors: Kagawa, T.F. / Jain, M. / Cooney, J.C. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7yzx.cif.gz | 265 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yzx.ent.gz | 159.7 KB | Display | PDB format |
PDBx/mmJSON format | 7yzx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7yzx_validation.pdf.gz | 465.3 KB | Display | wwPDB validaton report |
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Full document | 7yzx_full_validation.pdf.gz | 469.6 KB | Display | |
Data in XML | 7yzx_validation.xml.gz | 35.2 KB | Display | |
Data in CIF | 7yzx_validation.cif.gz | 51.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yz/7yzx ftp://data.pdbj.org/pub/pdb/validation_reports/yz/7yzx | HTTPS FTP |
-Related structure data
Related structure data | 3eifS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 109986.938 Da / Num. of mol.: 2 / Mutation: D783A Source method: isolated from a genetically manipulated source Details: Sequence begins with residue N31. Chain B is likely a peptide produced by autoproteolytic activation of the enzyme. Residues in this chain are in the propeptide region. Assignments of ...Details: Sequence begins with residue N31. Chain B is likely a peptide produced by autoproteolytic activation of the enzyme. Residues in this chain are in the propeptide region. Assignments of density for L83, A84, P85, Q86, and A87 in Chain B are tentative. Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: scpA / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: B6ETQ5, C5a peptidase |
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-Non-polymers , 5 types, 337 molecules
#2: Chemical | ChemComp-CA / | ||||
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#3: Chemical | ChemComp-NA / | ||||
#4: Chemical | ChemComp-SO4 / #5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 2.4 M ammonium sulfate and 0.2 M Tris/HCl pH 7.4-7.8 PH range: 7.4-7.8 |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96864 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 20, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96864 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→46.23 Å / Num. obs: 93718 / % possible obs: 99.72 % / Redundancy: 14 % / Biso Wilson estimate: 41.58 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1454 / Rpim(I) all: 0.04041 / Rrim(I) all: 0.1512 / Net I/σ(I): 12.34 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 13.3 % / Rmerge(I) obs: 4.47 / Mean I/σ(I) obs: 0.55 / Num. unique obs: 9050 / CC1/2: 0.188 / CC star: 0.562 / Rpim(I) all: 1.206 / Rrim(I) all: 4.639 / % possible all: 97.88 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3EIF Resolution: 1.9→45 Å / SU ML: 0.3046 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.4375 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.38 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→45 Å
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Refine LS restraints |
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LS refinement shell |
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