+Open data
-Basic information
Entry | Database: PDB / ID: 4yna | ||||||
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Title | Oxidized YfiR | ||||||
Components | YfiR | ||||||
Keywords | TRANSCRIPTION / Periplasmic Repressor Protein / oxidized form | ||||||
Function / homology | YfiR/HmsC-like / YfiR/HmsC-like / periplasmic space / Negative regulator YfiR Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa PAO1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Xu, M. / Jiang, T. | ||||||
Funding support | China, 1items
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Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2015 Title: Crystal structures of YfiR from Pseudomonas aeruginosa in two redox states Authors: Yang, X. / Yang, X.-A. / Xu, M. / Zhou, L. / Fan, Z. / Jiang, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4yna.cif.gz | 126.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yna.ent.gz | 98.3 KB | Display | PDB format |
PDBx/mmJSON format | 4yna.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yn/4yna ftp://data.pdbj.org/pub/pdb/validation_reports/yn/4yna | HTTPS FTP |
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-Related structure data
Related structure data | 4yn7SC 4yn9C S: Starting model for refinement C: citing same article (ref.) |
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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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-Components
#1: Protein | Mass: 17392.783 Da / Num. of mol.: 4 / Fragment: UNP residues 35-190 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: yfiR, PA1121 / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q9I4L4 #2: Chemical | |
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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: 2.28 Å3/Da / Density % sol: 46.06 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 1.8 M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.54187 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU / Detector: CCD / Date: Feb 14, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54187 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.2→50 Å / Num. obs: 10704 / % possible obs: 98.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.164 / Χ2: 0.969 / Net I/av σ(I): 10.424 / Net I/σ(I): 5.1 / Num. measured all: 74115 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4YN7 Resolution: 3.2→34.88 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.836 / SU B: 20.337 / SU ML: 0.373 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.687 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 249.82 Å2 / Biso mean: 94.62 Å2 / Biso min: 23.17 Å2
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Refinement step | Cycle: final / Resolution: 3.2→34.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.196→3.279 Å / Total num. of bins used: 20
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