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Yorodumi- PDB-6u1b: Structure of N-terminus locked Esp with eight pro-peptide residue... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6u1b | ||||||
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Title | Structure of N-terminus locked Esp with eight pro-peptide residues - V67C, D255C | ||||||
Components | Glutamyl endopeptidase | ||||||
Keywords | HYDROLASE / serine protease | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08008557193 Å | ||||||
Authors | Manne, K. / Sthanam, V.L.N. | ||||||
Funding support | United States, 1items
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Citation | Journal: Acta Crystallogr.,Sect.D / 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 | 6u1b.cif.gz | 71.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6u1b.ent.gz | 42.6 KB | Display | PDB format |
PDBx/mmJSON format | 6u1b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6u1b_validation.pdf.gz | 247.8 KB | Display | wwPDB validaton report |
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Full document | 6u1b_full_validation.pdf.gz | 247.8 KB | Display | |
Data in XML | 6u1b_validation.xml.gz | 929 B | Display | |
Data in CIF | 6u1b_validation.cif.gz | 4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u1/6u1b ftp://data.pdbj.org/pub/pdb/validation_reports/u1/6u1b | HTTPS FTP |
-Related structure data
Related structure data | 6pymSC 6tyaC 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: 24487.098 Da / Num. of mol.: 1 / Mutation: V67C, D255C 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 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 1 M Lithium Chloride, 0.1 M Tris pH 8.5, 20% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Mar 30, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.08→36.3514163239 Å / Num. obs: 12812 / % possible obs: 99 % / Redundancy: 2 % / Biso Wilson estimate: 19.2446709355 Å2 / CC1/2: 1 / Rrim(I) all: 0.014 / Net I/σ(I): 43.51 |
Reflection shell | Resolution: 2.08→2.154 Å / Rmerge(I) obs: 0.03804 / Num. unique obs: 1016 / CC1/2: 0.992 / Rrim(I) all: 0.05379 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6PYM Resolution: 2.08008557193→36.3514163239 Å / SU ML: 0.208011260955 / Cross valid method: NONE / σ(F): 1.44033640847 / Phase error: 20.3513751763
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.1474656215 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.08008557193→36.3514163239 Å
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Refine LS restraints |
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LS refinement shell |
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