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Yorodumi- PDB-5uvk: Serial Millisecond Crystallography of Membrane and Soluble Protei... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5uvk | |||||||||||||||||||||||||||
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Title | Serial Millisecond Crystallography of Membrane and Soluble Protein Micro-crystals using Synchrotron Radiation | |||||||||||||||||||||||||||
Components |
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Keywords | ELECTRON TRANSPORT / Multi-protein cofactor antenna complex | |||||||||||||||||||||||||||
Function / homology | Function and homology information phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis Similarity search - Function | |||||||||||||||||||||||||||
Biological species | Thermosynechococcus elongatus (bacteria) | |||||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | |||||||||||||||||||||||||||
Authors | Martin-Garcia, J.M. / Conrad, C.E. / Nelson, G. / Stander, N. / Zatsepin, N.A. / Zook, J. / Zhu, L. / Geiger, J. / Chun, E. / Kissick, D. ...Martin-Garcia, J.M. / Conrad, C.E. / Nelson, G. / Stander, N. / Zatsepin, N.A. / Zook, J. / Zhu, L. / Geiger, J. / Chun, E. / Kissick, D. / Hilgart, M.C. / Ogata, C. / Ishchenko, A. / Nagaratnam, N. / Roy-Chowdhury, S. / Coe, J. / Subramanian, G. / Schaffer, A. / James, D. / Ketawala, G. / Venugopalan, N. / Xu, S. / Corcoran, S. / Ferguson, D. / Weierstall, U. / Spence, J.C.H. / Cherezov, V. / Fromme, P. / Fischetti, R.F. / Liu, W. | |||||||||||||||||||||||||||
Funding support | United States, 8items
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Citation | Journal: Iucrj / Year: 2017 Title: Serial millisecond crystallography of membrane and soluble protein microcrystals using synchrotron radiation. Authors: Martin-Garcia, J.M. / Conrad, C.E. / Nelson, G. / Stander, N. / Zatsepin, N.A. / Zook, J. / Zhu, L. / Geiger, J. / Chun, E. / Kissick, D. / Hilgart, M.C. / Ogata, C. / Ishchenko, A. / ...Authors: Martin-Garcia, J.M. / Conrad, C.E. / Nelson, G. / Stander, N. / Zatsepin, N.A. / Zook, J. / Zhu, L. / Geiger, J. / Chun, E. / Kissick, D. / Hilgart, M.C. / Ogata, C. / Ishchenko, A. / Nagaratnam, N. / Roy-Chowdhury, S. / Coe, J. / Subramanian, G. / Schaffer, A. / James, D. / Ketwala, G. / Venugopalan, N. / Xu, S. / Corcoran, S. / Ferguson, D. / Weierstall, U. / Spence, J.C.H. / Cherezov, V. / Fromme, P. / Fischetti, R.F. / Liu, W. | |||||||||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5uvk.cif.gz | 81.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5uvk.ent.gz | 60.4 KB | Display | PDB format |
PDBx/mmJSON format | 5uvk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5uvk_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 5uvk_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 5uvk_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | 5uvk_validation.cif.gz | 20.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uv/5uvk ftp://data.pdbj.org/pub/pdb/validation_reports/uv/5uvk | HTTPS FTP |
-Related structure data
Related structure data | 5uviC 5uvjC 5uvlC 4zizS C: citing same article (ref.) 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
#1: Protein | Mass: 17456.631 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermosynechococcus elongatus (strain BP-1) (bacteria) Strain: BP-1 / Gene: cpcA, tlr1958 / Production host: Thermosynechococcus elongatus (bacteria) / References: UniProt: P50032 |
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#2: Protein | Mass: 18216.652 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermosynechococcus elongatus (strain BP-1) (bacteria) Strain: BP-1 / Gene: cpcB, tlr1957 / Production host: Thermosynechococcus elongatus (bacteria) / References: UniProt: P50033 |
#3: Chemical |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.18 % |
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Crystal grow | Temperature: 277 K / Method: batch mode / pH: 7 / Details: 75 mM HEPES pH 7, 20 mM MgCl2, 9 % PEG 3350 |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 16, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50.01 Å / Num. obs: 6280 / % possible obs: 99.7 % / Redundancy: 156.4 % / CC1/2: 0.986 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 3.1→3.18 Å / CC1/2: 0.799 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ZIZ Resolution: 3.1→50.01 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.916 / SU B: 18.652 / SU ML: 0.314 / Cross valid method: THROUGHOUT / ESU R Free: 0.433 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 48.046 Å2
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Refinement step | Cycle: 1 / Resolution: 3.1→50.01 Å
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Refine LS restraints |
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