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Yorodumi- PDB-4xxi: Crystal structure of the Bilin-binding domain of phycobilisome co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xxi | ||||||
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Title | Crystal structure of the Bilin-binding domain of phycobilisome core-membrane linker ApcE | ||||||
Components | Phycobiliprotein ApcE | ||||||
Keywords | TRANSFERASE / ApcE / phycobilisome / phycocyanobilin attachment | ||||||
Function / homology | Function and homology information Lyases / phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis / lyase activity Similarity search - Function | ||||||
Biological species | Nostoc sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Tang, K. / Ding, W.-L. / Hoppner, A. / Gartner, W. / Zhao, K.-H. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2015 Title: The terminal phycobilisome emitter, LCM: A light-harvesting pigment with a phytochrome chromophore Authors: Tang, K. / Ding, W.-L. / Hoppner, A. / Zhao, C. / Zhang, L. / Hontani, Y. / Kennis, J.T.M. / Gartner, W. / Scheer, H. / Zhou, M. / Zhao, K.-H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xxi.cif.gz | 74.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xxi.ent.gz | 54.7 KB | Display | PDB format |
PDBx/mmJSON format | 4xxi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xx/4xxi ftp://data.pdbj.org/pub/pdb/validation_reports/xx/4xxi | HTTPS FTP |
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-Related structure data
Related structure data | 4xxkSC 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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Unit cell |
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-Components
#1: Protein | Mass: 17677.100 Da / Num. of mol.: 2 Fragment: UNP residues 20-240, with deletion of residues 77-153 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nostoc sp. (strain PCC 7120 / UTEX 2576) (bacteria) Strain: PCC 7120 / UTEX 2576 / Gene: apcE, alr0020 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P80559 #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 2.39 Å3/Da / Density % sol: 48.55 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 HEPES, pH 7.0, 29% (w/v) PEG400, 0.2 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97092 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 16, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97092 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 17930 / % possible obs: 99.9 % / Redundancy: 8.5 % / Net I/σ(I): 25.4 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.215 / Mean I/σ(I) obs: 9 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4XXK Resolution: 2.2→40.276 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.66 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→40.276 Å
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Refine LS restraints |
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LS refinement shell |
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