+Open data
-Basic information
Entry | Database: PDB / ID: 2qfi | ||||||
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Title | Structure of the zinc transporter YiiP | ||||||
Components | Ferrous-iron efflux pump fieF | ||||||
Keywords | TRANSPORT PROTEIN / zinc transporter | ||||||
Function / homology | Function and homology information cadmium ion transport / zinc efflux active transmembrane transporter activity / zinc ion transport / cadmium ion transmembrane transporter activity / ferrous iron transmembrane transporter activity / intracellular zinc ion homeostasis / antiporter activity / iron ion transport / identical protein binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3.8 Å | ||||||
Authors | Lu, M. | ||||||
Citation | Journal: Science / Year: 2007 Title: Structure of the zinc transporter YiiP. Authors: Lu, M. / Fu, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qfi.cif.gz | 243.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qfi.ent.gz | 198.7 KB | Display | PDB format |
PDBx/mmJSON format | 2qfi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2qfi_validation.pdf.gz | 444.2 KB | Display | wwPDB validaton report |
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Full document | 2qfi_full_validation.pdf.gz | 560.1 KB | Display | |
Data in XML | 2qfi_validation.xml.gz | 37.9 KB | Display | |
Data in CIF | 2qfi_validation.cif.gz | 50.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qf/2qfi ftp://data.pdbj.org/pub/pdb/validation_reports/qf/2qfi | HTTPS FTP |
-Related structure data
Similar structure data |
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-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: TYR / Beg label comp-ID: TYR / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 1 / Auth seq-ID: 5 - 290 / Label seq-ID: 5 - 290
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-Components
#1: Protein | Mass: 32957.164 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fieF / Plasmid: pET15b / Cell line (production host): BL21/DE3 / Production host: Escherichia coli (E. coli) / References: UniProt: P69380 #2: Chemical | ChemComp-ZN / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 4 |
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-Sample preparation
Crystal | Density Matthews: 5.856 Å3/Da / Density % sol: 78.998 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Dec 1, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.8→30 Å / Num. all: 16000 / Num. obs: 15534 / % possible obs: 97.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6 % / Biso Wilson estimate: 100 Å2 / Rmerge(I) obs: 0.129 / Rsym value: 0.129 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 3.8→4 Å / Redundancy: 3 % / Rmerge(I) obs: 0.429 / Mean I/σ(I) obs: 1.9 / Num. unique all: 1000 / Rsym value: 0.429 / % possible all: 91.9 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 3.8→12 Å / Cor.coef. Fo:Fc: 0.883 / Cor.coef. Fo:Fc free: 0.904 / SU B: 71.277 / SU ML: 0.628 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.703 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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: 116.019 Å2
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Refinement step | Cycle: LAST / Resolution: 3.8→12 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: 2205 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 3.8→3.889 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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