+Open data
-Basic information
Entry | Database: PDB / ID: 2xxq | ||||||
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Title | A widespread family of bacterial cell wall assembly proteins | ||||||
Components | CPS2A | ||||||
Keywords | REPLICATION / PEPTIDOGLYCAN / LCP / LYTR | ||||||
Function / homology | Function and homology information | ||||||
Biological species | STREPTOCOCCUS PNEUMONIAE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å | ||||||
Authors | Marles-Wright, J. / Kawai, Y. / Emmins, R. / Ishikawa, S. / Kuwano, M. / Heinz, N. / Cleverley, R.M. / Bui, N.K. / Ogasawara, N. / Lewis, R.J. ...Marles-Wright, J. / Kawai, Y. / Emmins, R. / Ishikawa, S. / Kuwano, M. / Heinz, N. / Cleverley, R.M. / Bui, N.K. / Ogasawara, N. / Lewis, R.J. / Vollmer, W. / Daniel, R.A. / Errington, J. | ||||||
Citation | Journal: Embo J. / Year: 2011 Title: A Widespread Family of Bacterial Cell Wall Assembly Proteins. Authors: Kawai, Y. / Marles-Wright, J. / Cleverley, R.M. / Emmins, R. / Ishikawa, S. / Kuwano, M. / Heinz, N. / Bui, N.K. / Hoyland, C.N. / Ogasawara, N. / Lewis, R.J. / Vollmer, W. / Daniel, R.A. / Errington, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xxq.cif.gz | 176.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xxq.ent.gz | 138.9 KB | Display | PDB format |
PDBx/mmJSON format | 2xxq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xxq_validation.pdf.gz | 632.8 KB | Display | wwPDB validaton report |
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Full document | 2xxq_full_validation.pdf.gz | 636.7 KB | Display | |
Data in XML | 2xxq_validation.xml.gz | 20.2 KB | Display | |
Data in CIF | 2xxq_validation.cif.gz | 30.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xx/2xxq ftp://data.pdbj.org/pub/pdb/validation_reports/xx/2xxq | HTTPS FTP |
-Related structure data
Related structure data | 2xxpSC 3telC 3tepC 3tflC 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: 43911.133 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN, RESIDUES 98-481 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: D39 / Variant: SEROTYPE 2 / Plasmid: PET28B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: Q9ZII9 | ||||||||
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#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-ACT / | #4: Chemical | ChemComp-ZTP / ( | #5: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.65 % / Description: NONE |
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Crystal grow | pH: 4.6 / Details: 0.1 M SODIUM ACETATE PH 4.6, 8 % PEG W/V 4000 |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 29, 2010 / Details: MIRRORS |
Radiation | Monochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→43.88 Å / Num. obs: 44731 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 13.8 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 21.6 |
Reflection shell | Resolution: 1.77→1.87 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XXP Resolution: 1.77→37.64 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.037 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.338 Å2
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Refinement step | Cycle: LAST / Resolution: 1.77→37.64 Å
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Refine LS restraints |
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