+Open data
-Basic information
Entry | Database: PDB / ID: 6q12 | ||||||
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Title | Structure of pro-Esp mutant- S66V | ||||||
Components | Glutamyl endopeptidase | ||||||
Keywords | HYDROLASE / serine protease / zymogen | ||||||
Function / homology | Function and homology information glutamyl endopeptidase / serine-type endopeptidase activity / proteolysis / extracellular region Similarity search - Function | ||||||
Biological species | Staphylococcus epidermidis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Manne, K. / Narayana, S.V.L. | ||||||
Funding support | United States, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2020 Title: Structural insights into the role of the N-terminus in the activation and function of extracellular serine protease from Staphylococcus epidermidis. Authors: Manne, K. / Narayana, S.V.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6q12.cif.gz | 114.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6q12.ent.gz | 73.1 KB | Display | PDB format |
PDBx/mmJSON format | 6q12.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6q12_validation.pdf.gz | 428 KB | Display | wwPDB validaton report |
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Full document | 6q12_full_validation.pdf.gz | 430.1 KB | Display | |
Data in XML | 6q12_validation.xml.gz | 18.4 KB | Display | |
Data in CIF | 6q12_validation.cif.gz | 26.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q1/6q12 ftp://data.pdbj.org/pub/pdb/validation_reports/q1/6q12 | HTTPS FTP |
-Related structure data
Related structure data | 6q24C 6pymS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 27648.512 Da / Num. of mol.: 2 / Mutation: S66V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus epidermidis (strain ATCC 12228) (bacteria) Strain: ATCC 12228 / Gene: gseA, esp, SE_1543 / Production host: Escherichia coli (E. coli) / References: UniProt: P0C0Q2, glutamyl endopeptidase #2: Water | ChemComp-HOH / | |
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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: 1.77 Å3/Da / Density % sol: 30.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350, 0.225 M Ammonium Nitrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 10, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→42.51 Å / Num. obs: 18892 / % possible obs: 95 % / Redundancy: 1.5 % / Biso Wilson estimate: 11.8350592685 Å2 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.057 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.2→2.27 Å / Rmerge(I) obs: 0.088 / Num. unique obs: 1779 / CC1/2: 0.966 / Rrim(I) all: 0.125 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6PYM Resolution: 2.2→42.51 Å / SU ML: 0.2585 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.34
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.68 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→42.51 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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