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Yorodumi- PDB-6a4r: Crystal structure of aspartate bound peptidase E from Salmonella ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6a4r | ||||||
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Title | Crystal structure of aspartate bound peptidase E from Salmonella enterica | ||||||
Components | Peptidase E | ||||||
Keywords | HYDROLASE / S51 peptidase / peptidase E / dimer / active site / active site loop | ||||||
Function / homology | Function and homology information dipeptidase E / dipeptidase activity / serine-type peptidase activity / proteolysis / cytoplasm Similarity search - Function | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.828 Å | ||||||
Authors | Yadav, P. / Chandravanshi, K. / Goyal, V.D. / Singh, R. / Kumar, A. / Gokhale, S.M. / Makde, R.D. | ||||||
Citation | Journal: FEBS Lett. / Year: 2018 Title: Structure of Asp-bound peptidase E from Salmonella enterica: Active site at dimer interface illuminates Asp recognition. Authors: Yadav, P. / Goyal, V.D. / Gaur, N.K. / Kumar, A. / Gokhale, S.M. / Makde, R.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6a4r.cif.gz | 199 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6a4r.ent.gz | 156.8 KB | Display | PDB format |
PDBx/mmJSON format | 6a4r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6a4r_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6a4r_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6a4r_validation.xml.gz | 20.7 KB | Display | |
Data in CIF | 6a4r_validation.cif.gz | 29.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a4/6a4r ftp://data.pdbj.org/pub/pdb/validation_reports/a4/6a4r | HTTPS FTP |
-Related structure data
Related structure data | 6a4sC 1fy2S 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: 28596.221 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria) Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: pepE, STM4190 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P36936, dipeptidase E #2: Chemical | #3: 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: 2.15 Å3/Da / Density % sol: 42.79 % |
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Crystal grow | Temperature: 294 K / Method: microbatch / pH: 5.5 Details: 0.1 M Bis-tris pH 5.5, 0.2 M Sodium chloride, 31 % Peg 3350 PH range: 5.0 - 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97949 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 5, 2018 / Details: mirrors |
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.827→45.34 Å / Num. obs: 41754 / % possible obs: 96.2 % / Redundancy: 2.9 % / Biso Wilson estimate: 19.3 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.041 / Rrim(I) all: 0.07 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.83→1.87 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2142 / CC1/2: 0.74 / Rpim(I) all: 0.369 / Rrim(I) all: 0.601 / % possible all: 79.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FY2 Resolution: 1.828→41.605 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.1
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.828→41.605 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -11.8147 Å / Origin y: -0.4214 Å / Origin z: -21.3299 Å
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Refinement TLS group | Selection details: all |