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Yorodumi- PDB-3a2s: Crystal Structure of outer membrane protein PorB from Neisseria m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3a2s | |||||||||
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Title | Crystal Structure of outer membrane protein PorB from Neisseria meningitidis in complex with sucrose | |||||||||
Components | Outer membrane protein II | |||||||||
Keywords | MEMBRANE PROTEIN / Beta barrel / outer membrane protein / porin / Neisseria meningitidis / Cell membrane / Cell outer membrane / Ion transport / Membrane / Transmembrane / TRANSPORT PROTEIN / IMMUNE SYSTEM | |||||||||
Function / homology | Function and homology information porin activity / pore complex / monoatomic ion transmembrane transport / cell outer membrane Similarity search - Function | |||||||||
Biological species | Neisseria meningitidis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Tanabe, M. / Iverson, T.M. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Structural basis for solute transport, nucleotide regulation, and immunological recognition of Neisseria meningitidis PorB. Authors: Tanabe, M. / Nimigean, C.M. / Iverson, T.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3a2s.cif.gz | 85.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3a2s.ent.gz | 61.1 KB | Display | PDB format |
PDBx/mmJSON format | 3a2s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a2/3a2s ftp://data.pdbj.org/pub/pdb/validation_reports/a2/3a2s | HTTPS FTP |
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-Related structure data
Related structure data | 3vztC 3vzuC 3vzwC 3a2r C: citing same article (ref.) S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 38179.305 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: porB / Plasmid: pET21bPorB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) derivative / References: UniProt: Q5RT80*PLUS |
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#2: Polysaccharide | beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose / |
#3: Chemical | ChemComp-LDA / |
#4: Water | ChemComp-HOH / |
Sequence details | A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THIS SEQUENCE WILL BE ...A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THIS SEQUENCE WILL BE DEPOSITED IN THE SEQUENCE DATABASE. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.38 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 100mM MES, 50mM CsCl, 28-32% Jeffamine M-600, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.978 Å |
Detector | Date: Jan 20, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 20889 / % possible obs: 99.4 % / Redundancy: 5.6 % / Rsym value: 0.067 / Net I/σ(I): 22 |
Reflection shell | Resolution: 2.2→2.25 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 1446 / Rsym value: 0.364 / % possible all: 96.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3A2R 3a2r Resolution: 2.2→41.38 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.552 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.265 / ESU R Free: 0.214 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.705 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→41.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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