+Open data
-Basic information
Entry | Database: PDB / ID: 7bj3 | ||||||||||||
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Title | ScpA from Streptococcus pyogenes, S512A active site 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 / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||||||||
Authors | Kagawa, T.F. / O'Connell, M.R. / Cooney, J.C. | ||||||||||||
Funding support | Ireland, 3items
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Citation | Journal: Comput Struct Biotechnol J / Year: 2021 Title: Enzyme kinetic and binding studies identify determinants of specificity for the immunomodulatory enzyme ScpA, a C5a inactivating bacterial protease. Authors: Tecza, M. / Kagawa, T.F. / Jain, M. / Cooney, J.C. #1: Journal: Eur.J.Biochem. / Year: 2002 Title: Processing, stability, and kinetic parameters of C5a peptidase from Streptococcus pyogenes. Authors: Anderson, E.T. / Wetherell, M.G. / Winter, L.A. / Olmsted, S.B. / Cleary, P.P. / Matsuka, Y.V. #2: Journal: Acta Crystallogr D Struct Biol / Year: 2019 Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams / Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bj3.cif.gz | 242.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bj3.ent.gz | 151.5 KB | Display | PDB format |
PDBx/mmJSON format | 7bj3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7bj3_validation.pdf.gz | 462.6 KB | Display | wwPDB validaton report |
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Full document | 7bj3_full_validation.pdf.gz | 465.3 KB | Display | |
Data in XML | 7bj3_validation.xml.gz | 34 KB | Display | |
Data in CIF | 7bj3_validation.cif.gz | 48.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bj/7bj3 ftp://data.pdbj.org/pub/pdb/validation_reports/bj/7bj3 | HTTPS FTP |
-Related structure data
Related structure data | 3eifS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 110014.945 Da / Num. of mol.: 1 / Mutation: S512A Source method: isolated from a genetically manipulated source Details: Prior to crystallization, ScpA S512A was subjected to limited proteolysis by SpeB (cysteine protease from S. pyogenes) as described in Anderson et al. (2002). This removes the propepide, ...Details: Prior to crystallization, ScpA S512A was subjected to limited proteolysis by SpeB (cysteine protease from S. pyogenes) as described in Anderson et al. (2002). This removes the propepide, leaving K90 as the N-terminal residue. Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: scpA / Plasmid: pGEX-6P-3 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: B6ETQ5, C5a peptidase |
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-Non-polymers , 6 types, 199 molecules
#2: Chemical | ChemComp-CA / | ||
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#3: Chemical | ChemComp-NA / | ||
#4: Chemical | ChemComp-EPE / | ||
#5: Chemical | ChemComp-MLA / | ||
#6: Chemical | ChemComp-SO4 / #7: 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: 2.61 Å3/Da / Density % sol: 52.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 2.0 M Ammonium sulfate, 0.2 M Hepes/KOH pH 7.5 |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N |
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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: Jul 13, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→36.24 Å / Num. obs: 36554 / % possible obs: 100 % / Redundancy: 5.6 % / Biso Wilson estimate: 25.22 Å2 / CC1/2: 0.968 / Rpim(I) all: 0.125 / Rrim(I) all: 0.299 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2.6→2.72 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4386 / CC1/2: 0.499 / Rpim(I) all: 0.509 / Rrim(I) all: 1.213 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3EIF Resolution: 2.6→36.24 Å / SU ML: 0.3634 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.1321 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: 24.89 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→36.24 Å
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Refine LS restraints |
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LS refinement shell |
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