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Yorodumi- PDB-2prs: Structure and metal binding properties of ZnuA, a periplasmic zin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2prs | ||||||
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Title | Structure and metal binding properties of ZnuA, a periplasmic zinc transporter from Escherichia coli | ||||||
Components | High-affinity zinc uptake system protein znuA | ||||||
Keywords | METAL TRANSPORT / protein consists of two (beta/alfa)4 domains | ||||||
Function / homology | Function and homology information zinc ion import across plasma membrane / zinc ion transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / periplasmic space / cell adhesion / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Yatsunyk, L.A. / Kim, L.R. / Vorontsov, I.I. / Rosenzweig, A.C. | ||||||
Citation | Journal: J.Biol.Inorg.Chem. / Year: 2008 Title: Structure and metal binding properties of ZnuA, a periplasmic zinc transporter from Escherichia coli. Authors: Yatsunyk, L.A. / Easton, J.A. / Kim, L.R. / Sugarbaker, S.A. / Bennett, B. / Breece, R.M. / Vorontsov, I.I. / Tierney, D.L. / Crowder, M.W. / Rosenzweig, A.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2prs.cif.gz | 125.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2prs.ent.gz | 96.5 KB | Display | PDB format |
PDBx/mmJSON format | 2prs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pr/2prs ftp://data.pdbj.org/pub/pdb/validation_reports/pr/2prs | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Details | the biological assembly is a monomer |
-Components
#1: Protein | Mass: 31177.219 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P39172 #2: Chemical | #3: Chemical | ChemComp-IPA / | #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: 2.47 Å3/Da / Density % sol: 50.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 30 % (w/v) PEG 4000, 5 % isopropanol, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction |
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Diffraction source |
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Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 7, 2006 / Details: mirrors | ||||||||||||||||||||
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | ||||||||||||||||||||
Reflection | Resolution: 1.7→28.8 Å / Num. obs: 64618 / % possible obs: 97.2 % / Redundancy: 3.6 % / Biso Wilson estimate: 32.5 Å2 / Rsym value: 0.053 | ||||||||||||||||||||
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 3.1 % / Num. unique all: 5643 / Rsym value: 0.323 / % possible all: 85.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: ZnZnuA in space group P212121 Resolution: 1.7→28.8 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.924 / SU B: 2.508 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.12 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.48 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→28.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.701→1.745 Å / Total num. of bins used: 20
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