+Open data
-Basic information
Entry | Database: PDB / ID: 3nkc | ||||||
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Title | Crystal structure of AqpZ F43W,H174G,T183F | ||||||
Components | Aquaporin Z | ||||||
Keywords | TRANSPORT PROTEIN / aquaporin / integral membrane protein / selectivity filter mutants | ||||||
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 / molecular replacement / Resolution: 3.1 Å | ||||||
Authors | Savage, D.F. / O'Connell III, J.D. / Finer-Moore, J. / Stroud, R.M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Structural context shapes the aquaporin selectivity filter. Authors: Savage, D.F. / O'Connell, J.D. / Miercke, L.J. / Finer-Moore, J. / 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 | 3nkc.cif.gz | 184.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nkc.ent.gz | 148 KB | Display | PDB format |
PDBx/mmJSON format | 3nkc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nk/3nkc ftp://data.pdbj.org/pub/pdb/validation_reports/nk/3nkc | HTTPS FTP |
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-Related structure data
Related structure data | 3nk5C 3nkaC 2o9fS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 1 / Auth seq-ID: 1 - 228 / Label seq-ID: 4 - 231
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Details | The biological assembly is a tetramer, which can be generated from either chain using the crystallographic 4-fold axis |
-Components
#1: Protein | Mass: 24017.977 Da / Num. of mol.: 2 / Mutation: F43W,H173G,T183F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: aqpZ, b0875, bniP, JW0859 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: P60844 #2: Sugar | #3: 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: 3.57 Å3/Da / Density % sol: 65.54 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 25-30% PEG 2000 100 mM sodium cacodylate 50-100 mM MgCl2, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 103 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.97949 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 15, 2006 / Details: monochrometer | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Khozu double flat crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.1→92.892 Å / Num. all: 10963 / Num. obs: 10963 / % possible obs: 88 % / Observed criterion σ(I): 3 / Redundancy: 3 % / Rmerge(I) obs: 0.115 / Rsym value: 0.115 / Net I/σ(I): 10.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2O9F Resolution: 3.1→19.67 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.186 / WRfactor Rwork: 0.1717 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8705 / SU B: 39.145 / SU ML: 0.299 / SU R Cruickshank DPI: 0.3801 / SU Rfree: 0.4185 / Isotropic thermal model: restrained individual with TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.418 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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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 max: 112.49 Å2 / Biso mean: 67.397 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 3.1→19.67 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2739 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 3.1→3.179 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 |
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