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Yorodumi- PDB-3vzw: Crystal Structure of outer membrane protein PorB from Neisseria m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vzw | |||||||||
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Title | Crystal Structure of outer membrane protein PorB from Neisseria meningitidis in complex with galactose | |||||||||
Components | outer membrane proteins | |||||||||
Keywords | MEMBRANE PROTEIN / transport | |||||||||
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: 3.2 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 | 3vzw.cif.gz | 79.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vzw.ent.gz | 58 KB | Display | PDB format |
PDBx/mmJSON format | 3vzw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vzw_validation.pdf.gz | 450.9 KB | Display | wwPDB validaton report |
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Full document | 3vzw_full_validation.pdf.gz | 460.8 KB | Display | |
Data in XML | 3vzw_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 3vzw_validation.cif.gz | 19.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vz/3vzw ftp://data.pdbj.org/pub/pdb/validation_reports/vz/3vzw | HTTPS FTP |
-Related structure data
Related structure data | 3a2sC 3vztC 3vzuC 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
#1: Protein | Mass: 38179.305 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis (bacteria) / Strain: W135 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) derivative / References: UniProt: Q5RT80*PLUS | ||
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#2: Sugar | ChemComp-GAL / | ||
#3: Chemical | Sequence details | A SEQUENCE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.83 % |
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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: APS / Beamline: 21-ID-D / Wavelength: 0.978 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 31, 2009 |
Radiation | Monochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. all: 7136 / Num. obs: 6570 / % possible obs: 91.7 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 |
Reflection shell | Lowest resolution: 3.28 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 5.9 / Num. unique all: 264 / Rsym value: 0.148 / % possible all: 51.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3A2R 3a2r Resolution: 3.2→42.18 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.937 / Cross valid method: THROUGHOUT / ESU R Free: 0.546 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 125.775 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→42.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.283 Å / Total num. of bins used: 20
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