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Yorodumi- PDB-6hps: Near-infrared dual bioluminescence imaging in vivo using infra-lu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hps | ||||||
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Title | Near-infrared dual bioluminescence imaging in vivo using infra-luciferin | ||||||
Components | Luciferin 4-monooxygenase | ||||||
Keywords | FLUORESCENT PROTEIN / near-infrared Bioluminescence imaging / P. pyralis luciferase / ANL SUPERFAMILY / LIGASE / ADENYLATING ENZYMES / LUCIFERASE / DOMAIN ALTERNATION | ||||||
Function / homology | Function and homology information Photinus-luciferin 4-monooxygenase (ATP-hydrolyzing) activity / firefly luciferase / long-chain fatty acid-CoA ligase activity / fatty-acyl-CoA biosynthetic process / bioluminescence / peroxisome / protein-folding chaperone binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Photinus pyralis (common eastern firefly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Parkinson, G.N. / Stowe, C. / Anderson, J.C. | ||||||
Citation | Journal: Elife / Year: 2019 Title: Near-infrared dual bioluminescence imaging in mouse models of cancer using infraluciferin. Authors: Stowe, C.L. / Burley, T.A. / Allan, H. / Vinci, M. / Kramer-Marek, G. / Ciobota, D.M. / Parkinson, G.N. / Southworth, T.L. / Agliardi, G. / Hotblack, A. / Lythgoe, M.F. / Branchini, B.R. / ...Authors: Stowe, C.L. / Burley, T.A. / Allan, H. / Vinci, M. / Kramer-Marek, G. / Ciobota, D.M. / Parkinson, G.N. / Southworth, T.L. / Agliardi, G. / Hotblack, A. / Lythgoe, M.F. / Branchini, B.R. / Kalber, T.L. / Anderson, J.C. / Pule, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hps.cif.gz | 218.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hps.ent.gz | 174.3 KB | Display | PDB format |
PDBx/mmJSON format | 6hps.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6hps_validation.pdf.gz | 989.4 KB | Display | wwPDB validaton report |
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Full document | 6hps_full_validation.pdf.gz | 1006 KB | Display | |
Data in XML | 6hps_validation.xml.gz | 39.5 KB | Display | |
Data in CIF | 6hps_validation.cif.gz | 52.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hp/6hps ftp://data.pdbj.org/pub/pdb/validation_reports/hp/6hps | HTTPS FTP |
-Related structure data
Related structure data | 3iepS 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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-Components
#1: Protein | Mass: 59984.965 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Photinus pyralis (common eastern firefly) Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P08659, firefly luciferase #2: Chemical | Has ligand of interest | Y | |
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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: 2.27 Å3/Da / Density % sol: 45.79 % / Description: Thin flat plate |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 150 mM ammonium sulfate, 50 mM HEPES pH 7.0, 2% PEG 1000 |
-Data collection
Diffraction | Mean temperature: 105 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 28, 2017 |
Radiation | Monochromator: single bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91587 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→22.5 Å / Num. obs: 18228 / % possible obs: 94.2 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.227 / Net I/σ(I): 2.15 |
Reflection shell | Resolution: 3.1→3.21 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 1.07 / Num. unique obs: 1830 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3IEP Resolution: 3.1→17.86 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.858 / SU B: 39.298 / SU ML: 0.665 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.748 / 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: 103.92 Å2 / Biso mean: 36.955 Å2 / Biso min: 15.48 Å2
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Refinement step | Cycle: final / Resolution: 3.1→17.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.18 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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