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Yorodumi- PDB-4pnj: Recombinant Sperm Whale P6 Myoglobin Solved with Single Pulse Fre... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pnj | ||||||
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Title | Recombinant Sperm Whale P6 Myoglobin Solved with Single Pulse Free Electron Laser Data | ||||||
Components | Myoglobin | ||||||
Keywords | OXYGEN TRANSPORT / Myoglobin / Femtosecond X-ray Crystallography | ||||||
Function / homology | Function and homology information nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / oxygen binding / peroxidase activity / heme binding / extracellular exosome / metal ion binding Similarity search - Function | ||||||
Biological species | Physeter catodon (sperm whale) | ||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.36 Å | ||||||
Model details | Structure solved from data obtained from 739 crystals | ||||||
Authors | Cohen, A. / Gonzalez, A. / Lam, W. / Lyubimov, A. / Sauter, N. / Tsai, Y. / Uervirojnangkoorn, M. / Brunger, A. / Soltis, M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2014 Title: Goniometer-based femtosecond crystallography with X-ray free electron lasers. Authors: Cohen, A.E. / Soltis, S.M. / Gonzalez, A. / Aguila, L. / Alonso-Mori, R. / Barnes, C.O. / Baxter, E.L. / Brehmer, W. / Brewster, A.S. / Brunger, A.T. / Calero, G. / Chang, J.F. / Chollet, M. ...Authors: Cohen, A.E. / Soltis, S.M. / Gonzalez, A. / Aguila, L. / Alonso-Mori, R. / Barnes, C.O. / Baxter, E.L. / Brehmer, W. / Brewster, A.S. / Brunger, A.T. / Calero, G. / Chang, J.F. / Chollet, M. / Ehrensberger, P. / Eriksson, T.L. / Feng, Y. / Hattne, J. / Hedman, B. / Hollenbeck, M. / Holton, J.M. / Keable, S. / Kobilka, B.K. / Kovaleva, E.G. / Kruse, A.C. / Lemke, H.T. / Lin, G. / Lyubimov, A.Y. / Manglik, A. / Mathews, I.I. / McPhillips, S.E. / Nelson, S. / Peters, J.W. / Sauter, N.K. / Smith, C.A. / Song, J. / Stevenson, H.P. / Tsai, Y. / Uervirojnangkoorn, M. / Vinetsky, V. / Wakatsuki, S. / Weis, W.I. / Zadvornyy, O.A. / Zeldin, O.B. / Zhu, D. / Hodgson, K.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pnj.cif.gz | 124 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pnj.ent.gz | 96.4 KB | Display | PDB format |
PDBx/mmJSON format | 4pnj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4pnj_validation.pdf.gz | 800.7 KB | Display | wwPDB validaton report |
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Full document | 4pnj_full_validation.pdf.gz | 802 KB | Display | |
Data in XML | 4pnj_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | 4pnj_validation.cif.gz | 20.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pn/4pnj ftp://data.pdbj.org/pub/pdb/validation_reports/pn/4pnj | HTTPS FTP |
-Related structure data
Related structure data | 1vxaS 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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Details | biological unit is the same as asym. |
-Components
#1: Protein | Mass: 17366.148 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Physeter catodon (sperm whale) / Gene: MB / Production host: Escherichia coli (E. coli) / References: UniProt: P02185 | ||
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#2: Chemical | ChemComp-HEM / | ||
#3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.06 Å3/Da / Density % sol: 59.86 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 2.2 - 2.8M (NH4)2SO4 in 20mM TrisHCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: Y |
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Diffraction source | Source: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: XPP Details: The data was assembled from still diffraction patterns collected from 739 crystals at the LCLS beamline XPP, using 50fs pulses Wavelength: 1.31 Å |
Detector | Type: CS-PAD CXI-1 / Detector: PIXEL / Date: Dec 7, 2012 |
Radiation | Monochromator: None (SASE pulse) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.31 Å / Relative weight: 1 |
Reflection | Resolution: 1.36→39.15 Å / Num. obs: 43767 / % possible obs: 95.7 % / Redundancy: 25.1 % / Biso Wilson estimate: 15.24 Å2 / Net I/σ(I): 33.94 |
Reflection shell | Resolution: 1.36→1.37 Å / % possible obs: 52 % / Redundancy: 1.57 % / % possible all: 52 |
Serial crystallography measurement | Focal spot size: 50 µm2 / Photons per pulse: 1 Tphotons/pulse / Pulse duration: 30 fsec. / Pulse photon energy: 9.5 keV |
Serial crystallography sample delivery fixed target | Motion control: DCSS / Sample holding: polycarbonate grid Sample solvent: 8% NaCl, 0.1M Sodium Acetage pH 4.0, 100mM Gadoteridol Support base: goniometer |
Serial crystallography data reduction | Crystal hits: 932 / Frames indexed: 739 / Frames total: 932 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1VXA Resolution: 1.36→39.105 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 2.15 / Phase error: 18.92 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 54.79 Å2 / Biso mean: 20.7716 Å2 / Biso min: 11.01 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.36→39.105 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18
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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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