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Yorodumi- PDB-2w2e: 1.15 Angstrom crystal structure of P.pastoris aquaporin, Aqy1, in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2w2e | ||||||
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Title | 1.15 Angstrom crystal structure of P.pastoris aquaporin, Aqy1, in a closed conformation at pH 3.5 | ||||||
Components | AQUAPORIN PIP2-7 7 | ||||||
Keywords | MEMBRANE PROTEIN / YEAST / GATING | ||||||
Function / homology | Function and homology information water channel activity / endoplasmic reticulum membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | KOMAGATAELLA PASTORIS (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å | ||||||
Authors | Fischer, G. / Kosinska-Eriksson, U. / Aponte-Santamaria, C. / Palmgren, M. / Geijer, C. / Hedfalk, K. / Hohmann, S. / de Groot, B.L. / Neutze, R. / Lindkvist-Petersson, K. | ||||||
Citation | Journal: Plos Biol. / Year: 2009 Title: Crystal Structure of a Yeast Aquaporin at 1.15 A Reveals a Novel Gating Mechanism.1.15 A Authors: Fischer, G. / Kosinska-Eriksson, U. / Aponte-Santamaria, C. / Palmgren, M. / Geijer, C. / Hedfalk, K. / Hohmann, S. / De Groot, B.L. / Neutze, R. / Lindkvist-Petersson, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2w2e.cif.gz | 126.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w2e.ent.gz | 98 KB | Display | PDB format |
PDBx/mmJSON format | 2w2e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2w2e_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 2w2e_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 2w2e_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 2w2e_validation.cif.gz | 20.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w2/2w2e ftp://data.pdbj.org/pub/pdb/validation_reports/w2/2w2e | HTTPS FTP |
-Related structure data
Related structure data | 2w1pC 1j4nS 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: 29932.436 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) KOMAGATAELLA PASTORIS (fungus) / Strain: X33 / References: UniProt: F2QVG4 | ||||
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#2: Sugar | ChemComp-BOG / #3: Chemical | #4: 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: 2.43 Å3/Da / Density % sol: 49.4 % / Description: NONE |
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Crystal grow | pH: 3.5 Details: 28% PEG400, 100 MM SODIUM CITRATE PH=3.5, 200 MM LITHIUM SULFATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 8, 2007 / Details: MIRRORS |
Radiation | Monochromator: SI 111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→20 Å / Num. obs: 111455 / % possible obs: 94.7 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.31 |
Reflection shell | Resolution: 1.15→1.2 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.16 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1J4N Resolution: 1.15→20 Å / Num. parameters: 20766 / Num. restraintsaints: 27331 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: H-ATOMS ADDED TO ALL RESIDUES AS A RIDING MODEL, EXCEPT TO THE ONES SURROUNDING THE WATER CHANNEL TO BE ABLE TO OBSERVE DIFFERENCE IN DENSITY. SIDECHAINS OF RESIDUES GLN12, GLU14 AND ARG236 ...Details: H-ATOMS ADDED TO ALL RESIDUES AS A RIDING MODEL, EXCEPT TO THE ONES SURROUNDING THE WATER CHANNEL TO BE ABLE TO OBSERVE DIFFERENCE IN DENSITY. SIDECHAINS OF RESIDUES GLN12, GLU14 AND ARG236 COULD NOT BE OBSERVED WITH SUFFICIENT OCCUPANCY - OCCUPANCY FOR THE NON-OBSERVED ATOMS WAS SET TO 0. SIDE-CHAINS OF RESIDUES ASP77 AND ARG123 COULD ONLY BE OBSERVED WITH PARTIAL OCCUPANCY AND THUS SET TO AN OCCUPANCY OF 0.5. 10 N-TERMINAL AND 6 C-TERMINAL RESIDUES COULD NOT BE OBSERVED.
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Refine analyze | Num. disordered residues: 9 / Occupancy sum hydrogen: 1936.39 / Occupancy sum non hydrogen: 2192.03 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.15→20 Å
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Refine LS restraints |
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