+Open data
-Basic information
Entry | Database: PDB / ID: 5j1k | ||||||
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Title | Crystal structure of Csd2-Csd2 dimer | ||||||
Components | ToxR-activated gene (TagE) | ||||||
Keywords | HYDROLASE / M23B family metallopeptidase / Homodimer | ||||||
Function / homology | Peptidase M23 / Peptidase family M23 / Duplicated hybrid motif / septum digestion after cytokinesis / cell division site / cell outer membrane / metalloendopeptidase activity / ToxR-activated gene (TagE) Function and homology information | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å | ||||||
Authors | An, D.R. / Suh, S.W. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Plos One / Year: 2016 Title: Structural Basis of the Heterodimer Formation between Cell Shape-Determining Proteins Csd1 and Csd2 from Helicobacter pylori Authors: An, D.R. / Im, H.N. / Jang, J.Y. / Kim, H.S. / Kim, J. / Yoon, H.J. / Hesek, D. / Lee, M. / Mobashery, S. / Kim, S.J. / Suh, S.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5j1k.cif.gz | 53.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5j1k.ent.gz | 37.3 KB | Display | PDB format |
PDBx/mmJSON format | 5j1k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5j1k_validation.pdf.gz | 440.5 KB | Display | wwPDB validaton report |
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Full document | 5j1k_full_validation.pdf.gz | 441.8 KB | Display | |
Data in XML | 5j1k_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | 5j1k_validation.cif.gz | 13.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j1/5j1k ftp://data.pdbj.org/pub/pdb/validation_reports/j1/5j1k | HTTPS FTP |
-Related 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: 24458.762 Da / Num. of mol.: 1 / Fragment: UNP residues 125-308 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: ATCC 700392 / 26695 / Gene: HP_1544 / Production host: Escherichia coli (E. coli) / References: UniProt: O26069 | ||
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#2: Chemical | #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: 2.35 Å3/Da / Density % sol: 47.73 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / Details: HEPES, Jeffamine ED-2001 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 7, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50.01 Å / Num. obs: 22028 / % possible obs: 99.8 % / Redundancy: 16.4 % / Net I/σ(I): 47.1 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 17 % / Mean I/σ(I) obs: 6.9 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→50.01 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.927 / SU B: 2.114 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.11 / 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: 22.801 Å2
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Refinement step | Cycle: 1 / Resolution: 1.81→50.01 Å
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Refine LS restraints |
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