+Open data
-Basic information
Entry | Database: PDB / ID: 4cqh | ||||||
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Title | Structure of Infrared Fluorescent Protein IFP2.0 | ||||||
Components | BACTERIOPHYTOCHROME | ||||||
Keywords | FLUORESCENT PROTEIN / INFRARED FLUORESCENT PROTEIN | ||||||
Function / homology | Function and homology information osmosensory signaling via phosphorelay pathway / detection of visible light / phosphorelay response regulator activity / protein kinase activator activity / histidine kinase / photoreceptor activity / phosphorelay sensor kinase activity / regulation of DNA-templated transcription / ATP binding / identical protein binding Similarity search - Function | ||||||
Biological species | DEINOCOCCUS RADIODURANS (radioresistant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 Å | ||||||
Authors | Lafaye, C. / Yu, D. / Noirclerc-Savoye, M. / Shu, X. / Royant, A. | ||||||
Citation | Journal: Nat.Commun. / Year: 2014 Title: An Improved Monomeric Infrared Fluorescent Protein for Neuronal and Tumour Brain Imaging. Authors: Yu, D. / Gustafson, W.C. / Han, C. / Lafaye, C. / Noirclerc-Savoye, M. / Ge, W. / Thayer, D.A. / Huang, H. / Kornberg, T.B. / Royant, A. / Jan, L.Y. / Jan, Y.N. / Weiss, W.A. / Shu, X. #1: Journal: Science / Year: 2009 Title: Mammalian Expression of Infrared Fluorescent Proteins Engineered from a Bacterial Phytochrome. Authors: Shu, X. / Royant, A. / Lin, M.Z. / Aguilera, T.A. / Lev-Ram, V. / Steinbach, P.A. / Tsien, R.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cqh.cif.gz | 152.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cqh.ent.gz | 119.2 KB | Display | PDB format |
PDBx/mmJSON format | 4cqh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4cqh_validation.pdf.gz | 758.6 KB | Display | wwPDB validaton report |
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Full document | 4cqh_full_validation.pdf.gz | 760.9 KB | Display | |
Data in XML | 4cqh_validation.xml.gz | 16.9 KB | Display | |
Data in CIF | 4cqh_validation.cif.gz | 25.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cq/4cqh ftp://data.pdbj.org/pub/pdb/validation_reports/cq/4cqh | HTTPS FTP |
-Related structure data
Related structure data | 2o9cS 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 35991.969 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-317 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) DEINOCOCCUS RADIODURANS (radioresistant) Plasmid: PBAD / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: Q9RZA4 |
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#2: Chemical | ChemComp-LBV / |
#3: Chemical | ChemComp-NA / |
#4: Water | ChemComp-HOH / |
Sequence details | IFP2.0 HAS BEEN ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.78 % / Description: NONE |
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Crystal grow | pH: 4.6 / Details: 30% PEG 400, 100 MM SODIUM ACETATE PH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 17, 2013 / Details: KB MIRRORS |
Radiation | Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 1.14→46.3 Å / Num. obs: 114179 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.14→1.16 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.1 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2O9C Resolution: 1.14→27.33 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.971 / SU B: 0.892 / SU ML: 0.019 / Cross valid method: THROUGHOUT / ESU R: 0.028 / ESU R Free: 0.029 / 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 mean: 14.151 Å2
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Refinement step | Cycle: LAST / Resolution: 1.14→27.33 Å
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Refine LS restraints |
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