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Yorodumi- PDB-6cxd: Crystal structure of peptidase B from Yersinia pestis CO92 at 2.7... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6cxd | ||||||
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Title | Crystal structure of peptidase B from Yersinia pestis CO92 at 2.75 A resolution | ||||||
Components | Peptidase B | ||||||
Keywords | HYDROLASE / peptidase B / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | Function and homology information PepB aminopeptidase / metalloaminopeptidase activity / manganese ion binding / transcription cis-regulatory region binding / cytoplasm Similarity search - Function | ||||||
Biological species | Yersinia pestis CO92 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Woinska, M. / Lipowska, J. / Shabalin, I.G. / Cymborowski, M. / Grimshaw, S. / Winsor, J. / Shuvalova, L. / Satchell, K.J. / Joachimiak, A. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Funding support | United States, 1items
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Citation | Journal: Febs J. / Year: 2020 Title: Structural and biochemical analysis of Bacillus anthracis prephenate dehydrogenase reveals an unusual mode of inhibition by tyrosine via the ACT domain. Authors: Shabalin, I.G. / Gritsunov, A. / Hou, J. / Slawek, J. / Miks, C.D. / Cooper, D.R. / Minor, W. / Christendat, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6cxd.cif.gz | 175.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cxd.ent.gz | 137.6 KB | Display | PDB format |
PDBx/mmJSON format | 6cxd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6cxd_validation.pdf.gz | 439.3 KB | Display | wwPDB validaton report |
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Full document | 6cxd_full_validation.pdf.gz | 440.3 KB | Display | |
Data in XML | 6cxd_validation.xml.gz | 16 KB | Display | |
Data in CIF | 6cxd_validation.cif.gz | 21.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cx/6cxd ftp://data.pdbj.org/pub/pdb/validation_reports/cx/6cxd | HTTPS FTP |
-Related structure data
Related structure data | 5uyyC 5v0sC 6u60C 3ij3S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 49323.301 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia pestis CO92 (bacteria) / Gene: pepB, YPO2889, y1342, YP_2566 / Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-Magic / References: UniProt: P58475, PepB aminopeptidase | ||
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#2: Chemical | ChemComp-SO4 / #3: 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: 2.42 Å3/Da / Density % sol: 49.16 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 uL 14 mg/mL protein in 20 mM Tris-HCl pH 7.5, 150 mM sodium chloride, 10% glycerol, 0.1% sodium azide, 0.5 mM TCEP, 1 mM ZnCl2 + 0.2 uL TOP96 #29 (0.2 M ammonium sulfate, 0.1 M sodium ...Details: 0.2 uL 14 mg/mL protein in 20 mM Tris-HCl pH 7.5, 150 mM sodium chloride, 10% glycerol, 0.1% sodium azide, 0.5 mM TCEP, 1 mM ZnCl2 + 0.2 uL TOP96 #29 (0.2 M ammonium sulfate, 0.1 M sodium cacodylate, 30% w/v PEG8000) against 1.5 M sodium chloride, 96-well 3-drop crystallization plate (Swissci) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 18, 2016 |
Radiation | Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→50 Å / Num. obs: 12769 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 10.8 % / Biso Wilson estimate: 60.7 Å2 / Rmerge(I) obs: 0.152 / Rsym value: 0.152 / Net I/av σ(I): 16.5 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 2.75→2.8 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.666 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 600 / CC1/2: 0.928 / Rsym value: 0.666 / % possible all: 94.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3IJ3 Resolution: 2.75→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.907 / SU B: 29.699 / SU ML: 0.28 / Cross valid method: THROUGHOUT / ESU R Free: 0.363 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.504 Å2
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Refinement step | Cycle: 1 / Resolution: 2.75→50 Å
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Refine LS restraints |
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