+Open data
-Basic information
Entry | Database: PDB / ID: 2o9d | |||||||||
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Title | Crystal Structure of AqpZ mutant T183C. | |||||||||
Components | Aquaporin Z | |||||||||
Keywords | MEMBRANE PROTEIN / aquaporin / integral membrane protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Center for Structures of Membrane Proteins / CSMP | |||||||||
Function / homology | Function and homology information intracellular water homeostasis / water transport / water channel activity / response to osmotic stress / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Savage, D.F. / Stroud, R.M. / Center for Structures of Membrane Proteins (CSMP) | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Structural basis of aquaporin inhibition by mercury. Authors: Savage, D.F. / Stroud, R.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2o9d.cif.gz | 99.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2o9d.ent.gz | 75.6 KB | Display | PDB format |
PDBx/mmJSON format | 2o9d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2o9d_validation.pdf.gz | 932.9 KB | Display | wwPDB validaton report |
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Full document | 2o9d_full_validation.pdf.gz | 940.3 KB | Display | |
Data in XML | 2o9d_validation.xml.gz | 19.8 KB | Display | |
Data in CIF | 2o9d_validation.cif.gz | 28 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o9/2o9d ftp://data.pdbj.org/pub/pdb/validation_reports/o9/2o9d | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / Refine code: 4
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-Components
#1: Protein | Mass: 23983.875 Da / Num. of mol.: 2 / Mutation: C9S,C20S,T183C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: aqpZ, bniP / Production host: Escherichia coli (E. coli) / References: UniProt: P60844 #2: Sugar | #3: Sugar | ChemComp-HSH / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.48 Å3/Da / Density % sol: 64.68 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.5 Details: hanging drop with 1:1 addition of protien and mothor liquor, 25% polyethylene glycol monomethyl ether 2000, 100 mM sodium cacodylate, 100 mM MgCl2, pH 6.5, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Detector | Type: ADSC QUANTUM 210 / Detector: CCD | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.11587 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→92.45 Å / Num. obs: 28901 / % possible obs: 98.3 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 6.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→92.45 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.932 / SU B: 16.283 / SU ML: 0.188 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.238 / ESU R Free: 0.201 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.666 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→92.45 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: B / Ens-ID: 1 / Number: 1649 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Selection: ALL
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