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Yorodumi- PDB-3cn5: Crystal structure of the Spinach Aquaporin SoPIP2;1 S115E, S274E ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cn5 | ||||||
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Title | Crystal structure of the Spinach Aquaporin SoPIP2;1 S115E, S274E mutant | ||||||
Components | Aquaporin | ||||||
Keywords | TRANSPORT PROTEIN / membrane protein / aquaporin / Transmembrane / Transport | ||||||
Function / homology | Function and homology information water channel activity / plasmodesma / vacuole / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Spinacia oleracea (spinach) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Nyblom, M. / Alfredsson, A. / Hallgren, K. / Hedfalk, K. / Neutze, R. / Tornroth-Horsefield, S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Structural and functional analysis of SoPIP2;1 mutants adds insight into plant aquaporin gating. Authors: Nyblom, M. / Frick, A. / Wang, Y. / Ekvall, M. / Hallgren, K. / Hedfalk, K. / Neutze, R. / Tajkhorshid, E. / Tornroth-Horsefield, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cn5.cif.gz | 60.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cn5.ent.gz | 43.4 KB | Display | PDB format |
PDBx/mmJSON format | 3cn5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3cn5_validation.pdf.gz | 414.4 KB | Display | wwPDB validaton report |
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Full document | 3cn5_full_validation.pdf.gz | 416.9 KB | Display | |
Data in XML | 3cn5_validation.xml.gz | 11.3 KB | Display | |
Data in CIF | 3cn5_validation.cif.gz | 15.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cn/3cn5 ftp://data.pdbj.org/pub/pdb/validation_reports/cn/3cn5 | HTTPS FTP |
-Related structure data
Related structure data | 3cllC 3cn6C 1z98S 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 32642.828 Da / Num. of mol.: 1 / Mutation: S115E, S274E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Spinacia oleracea (spinach) / Production host: Pichia pastoris (fungus) / Strain (production host): X33 / References: UniProt: Q41372 |
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#2: 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: 2.53 Å3/Da / Density % sol: 51.48 % |
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Crystal grow | Temperature: 280 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 30% PEG400, 0.1M NaCl, 0.1M MgCl2, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 280K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 2, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→20 Å / Num. all: 20465 / Num. obs: 20465 / % possible obs: 100 % / Redundancy: 7.7 % / Rsym value: 0.084 |
Reflection shell | Resolution: 2.05→2.16 Å / Redundancy: 7.6 % / Num. unique all: 3007 / Rsym value: 0.335 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1Z98 Resolution: 2.05→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.604 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 26.465 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.103 Å / Total num. of bins used: 20
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