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- PDB-3vzu: Crystal Structure of outer membrane protein PorB from Neisseria m... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3vzu | |||||||||
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Title | Crystal Structure of outer membrane protein PorB from Neisseria meningitidis in complex with AMP-PNP | |||||||||
![]() | outer membrane protein | |||||||||
![]() | MEMBRANE PROTEIN / Beta-barrel / porin / channel / outer membrane protein / transport | |||||||||
Function / homology | ![]() porin activity / pore complex / monoatomic ion transmembrane transport / cell outer membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Tanabe, M. / Iverson, T.M. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 80.3 KB | Display | ![]() |
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PDB format | ![]() | 58.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 804.1 KB | Display | ![]() |
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Full document | ![]() | 818.3 KB | Display | |
Data in XML | ![]() | 16.3 KB | Display | |
Data in CIF | ![]() | 21.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3a2sC ![]() 3vztC ![]() 3vzwC ![]() 3a2r C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-ANP / |
Sequence details | A SEQUENCE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.12 % |
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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: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 31, 2009 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→42.26 Å / Num. all: 9609 / Num. obs: 8668 / % possible obs: 91.7 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 |
Reflection shell | Resolution: 2.9→2.97 Å / Redundancy: 6 % / Mean I/σ(I) obs: 3.6 / Rsym value: 0.338 / % possible all: 47 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3A2R ![]() 3a2r Resolution: 2.9→39.26 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.931 / Cross valid method: THROUGHOUT / ESU R Free: 0.471 / 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: 106.663 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→39.26 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.901→2.976 Å / Total num. of bins used: 20
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