+Open data
-Basic information
Entry | Database: PDB / ID: 5my7 | ||||||
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Title | Adhesin Complex Protein from Neisseria meningitidis | ||||||
Components | Adhesin | ||||||
Keywords | CELL ADHESION / lysozyme / Neisseria meningitidis / antigen | ||||||
Function / homology | DI(HYDROXYETHYL)ETHER / Adhesin / Adhesin complex protein Function and homology information | ||||||
Biological species | Neisseria meningitidis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.4 Å | ||||||
Authors | Derrick, J.P. / Awanye, A. | ||||||
Citation | Journal: PLoS Pathog. / Year: 2017 Title: Structure of the Neisseria Adhesin Complex Protein (ACP) and its role as a novel lysozyme inhibitor. Authors: Humbert, M.V. / Awanye, A.M. / Lian, L.Y. / Derrick, J.P. / Christodoulides, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5my7.cif.gz | 48.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5my7.ent.gz | 36.9 KB | Display | PDB format |
PDBx/mmJSON format | 5my7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5my7_validation.pdf.gz | 426.9 KB | Display | wwPDB validaton report |
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Full document | 5my7_full_validation.pdf.gz | 426.9 KB | Display | |
Data in XML | 5my7_validation.xml.gz | 6.3 KB | Display | |
Data in CIF | 5my7_validation.cif.gz | 7.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/my/5my7 ftp://data.pdbj.org/pub/pdb/validation_reports/my/5my7 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 13305.372 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Sequence includes signal peptide / Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: N875_06250 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A8F5R9, UniProt: Q9JXD8*PLUS | ||||
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#2: Chemical | #3: Chemical | ChemComp-NA / | #4: 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: 1.91 Å3/Da / Density % sol: 35.68 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 25 mM Hepes/Na pH 7.5, 37 mM NaCl) with 200 nl precipitant solution containing 0.2 M lithium sulfate, 0.1 M sodium acetate pH 4.5 and 50 % w/v PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 11, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9282 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50.64 Å / Num. obs: 20461 / % possible obs: 99.9 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.036 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 6 % / Rmerge(I) obs: 0.997 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1001 / Rpim(I) all: 0.668 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 1.4→50.64 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.179 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.057 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.968 Å2
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Refinement step | Cycle: 1 / Resolution: 1.4→50.64 Å
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Refine LS restraints |
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