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Yorodumi- PDB-6cuj: Crystal structure of the C-terminal domain of neisserial heparin ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6cuj | ||||||
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Title | Crystal structure of the C-terminal domain of neisserial heparin binding antigen (NHBA) | ||||||
Components | Gna2132 | ||||||
Keywords | LIPID BINDING PROTEIN / Vaccine / Neisseria / Meningitis / Disorder | ||||||
Function / homology | Transferrin-binding protein B, C-lobe/N-lobe beta barrel domain / C-lobe and N-lobe beta barrels of Tf-binding protein B / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / cell outer membrane / Prokaryotic membrane lipoprotein lipid attachment site profile. / heparin binding / cell adhesion / DNA binding / Neisserial heparin binding antigen Function and homology information | ||||||
Biological species | Neisseria meningitidis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.805 Å | ||||||
Authors | Malito, E. / Spraggon, G. | ||||||
Citation | Journal: PLoS ONE / Year: 2018 Title: Structures of NHBA elucidate a broadly conserved epitope identified by a vaccine induced antibody. Authors: Maritan, M. / Veggi, D. / Cozzi, R. / Dello Iacono, L. / Bartolini, E. / Lo Surdo, P. / Maruggi, G. / Spraggon, G. / Bottomley, M.J. / Malito, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6cuj.cif.gz | 71.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cuj.ent.gz | 52.8 KB | Display | PDB format |
PDBx/mmJSON format | 6cuj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6cuj_validation.pdf.gz | 434.2 KB | Display | wwPDB validaton report |
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Full document | 6cuj_full_validation.pdf.gz | 436.2 KB | Display | |
Data in XML | 6cuj_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 6cuj_validation.cif.gz | 18.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cu/6cuj ftp://data.pdbj.org/pub/pdb/validation_reports/cu/6cuj | HTTPS FTP |
-Related structure data
Related structure data | 5nyxC 5o1rC 2lfuS 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: 17377.043 Da / Num. of mol.: 2 / Fragment: UNP Residues 133-427 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: gna2132, nhba, A6J54_02980 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9JPP1 #2: Water | ChemComp-HOH / | Sequence details | The full sequence MAANGGSNFGRVDLANGVLIDGPSQNITLTHSKGDSSNGDNLLDEEAPSKSEFENLNESERIEKYKKDGKSDKFTNLVAT ...The full sequence MAANGGSNFG | |
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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: 2.49 Å3/Da / Density % sol: 50 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3,350, 0.2 M Sodium thiocyanate |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.96862 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 29, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96862 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→46 Å / Num. obs: 31127 / % possible obs: 99.9 % / Redundancy: 4.6 % / Biso Wilson estimate: 32.8 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.06 / Rsym value: 0.06 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.8→1.91 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 2 / Num. unique obs: 5025 / CC1/2: 0.84 / Rsym value: 0.47 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2LFU Resolution: 1.805→46 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.18
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.805→46 Å
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Refine LS restraints |
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LS refinement shell |
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