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Yorodumi- PDB-4q7o: The crystal structure of an immunity protein NMB0503 from Neisser... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4q7o | ||||||
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Title | The crystal structure of an immunity protein NMB0503 from Neisseria meningitidis MC58 | ||||||
Components | Immunity protein | ||||||
Keywords | IMMUNE SYSTEM / structural genomics / PSI-Biology / protein structure initiative / MCSG / Midwest Center for Structural Genomics / Structure-Function Analysis of Polymorphic CDI Toxin-Immunity Protein Complexes / UC4CDI | ||||||
Function / homology | BROMIDE ION / FORMIC ACID / Uncharacterized protein Function and homology information | ||||||
Biological species | Neisseria meningitidis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å | ||||||
Authors | Tan, K. / Stols, L. / Eschenfeldt, W. / Babnigg, G. / Low, D.A. / Hayes, C.S. / Goulding, C.W. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Structure-Function Analysis of Polymorphic CDI Toxin-Immunity Protein Complexes (UC4CDI) | ||||||
Citation | Journal: Acta Crystallogr F Struct Biol Commun / Year: 2015 Title: The structure of a contact-dependent growth-inhibition (CDI) immunity protein from Neisseria meningitidis MC58. Authors: Tan, K. / Johnson, P.M. / Stols, L. / Boubion, B. / Eschenfeldt, W. / Babnigg, G. / Hayes, C.S. / Joachimiak, A. / Goulding, C.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4q7o.cif.gz | 134.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4q7o.ent.gz | 104.7 KB | Display | PDB format |
PDBx/mmJSON format | 4q7o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4q7o_validation.pdf.gz | 448.5 KB | Display | wwPDB validaton report |
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Full document | 4q7o_full_validation.pdf.gz | 450.1 KB | Display | |
Data in XML | 4q7o_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | 4q7o_validation.cif.gz | 21.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q7/4q7o ftp://data.pdbj.org/pub/pdb/validation_reports/q7/4q7o | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 17016.076 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis (bacteria) / Strain: MC58 / Gene: NMB0503 / Plasmid: pMCSG58 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q7DDN8 #2: Chemical | ChemComp-BR / #3: Chemical | #4: 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: 2.11 Å3/Da / Density % sol: 41.7 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2M MgCl, 0.1M Bis-Tris:HCl, 25% (w/v) PEG3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.91928 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 3, 2013 / Details: mirror |
Radiation | Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91928 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→30 Å / Num. all: 49973 / Num. obs: 49973 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -5 / Redundancy: 3.4 % / Biso Wilson estimate: 10.34 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 24.4 |
Reflection shell | Resolution: 1.45→1.48 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 2.76 / Num. unique all: 2352 / % possible all: 94.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.45→29.556 Å / SU ML: 0.12 / σ(F): 1.35 / Phase error: 16.77 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→29.556 Å
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Refine LS restraints |
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LS refinement shell |
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