+Open data
-Basic information
Entry | Database: PDB / ID: 7f86 | ||||||
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Title | Crystal structure of Phycoerythrin from Halomicronema Sp. R31DM | ||||||
Components |
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Keywords | PHOTOSYNTHESIS / Light harvesting / Phycobiliproteins / Cyanobacteria | ||||||
Function / homology | PHYCOERYTHROBILIN Function and homology information | ||||||
Biological species | Halomicronema sp. R31DM (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å | ||||||
Authors | Patel, S.N. / Gupta, G.D. / Sonani, R.R. / Singh, N.K. / Kumar, V. / Madamwar, D. | ||||||
Funding support | India, 1items
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Citation | Journal: J.Biomol.Struct.Dyn. / Year: 2023 Title: Crystal structure analysis of phycoerythrin from marine cyanobacterium Halomicronema . Authors: Patel, S.N. / Sonani, R.R. / Gupta, G.D. / Singh, N.K. / Kumar, V. / Madamwar, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7f86.cif.gz | 865.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7f86.ent.gz | 735.3 KB | Display | PDB format |
PDBx/mmJSON format | 7f86.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7f86_validation.pdf.gz | 18.3 MB | Display | wwPDB validaton report |
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Full document | 7f86_full_validation.pdf.gz | 18.3 MB | Display | |
Data in XML | 7f86_validation.xml.gz | 196.8 KB | Display | |
Data in CIF | 7f86_validation.cif.gz | 256.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f8/7f86 ftp://data.pdbj.org/pub/pdb/validation_reports/f8/7f86 | HTTPS FTP |
-Related structure data
Related structure data | 5nb4S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 19367.168 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Halomicronema sp. R31DM (bacteria) #2: Protein | Mass: 17760.973 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Halomicronema sp. R31DM (bacteria) #3: Chemical | ChemComp-PEB / #4: Water | ChemComp-HOH / | 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: 2.68 Å3/Da / Density % sol: 54.07 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.2 M Potassium sodium tartrate, 20% (W/V) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.979 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 5, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.21→42.17 Å / Num. obs: 225119 / % possible obs: 97.3 % / Redundancy: 3.9 % / CC1/2: 0.997 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 2.21→2.21 Å / Num. unique obs: 11005 / CC1/2: 0.974 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5NB4 Resolution: 2.21→42.17 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.91 / SU B: 4.803 / SU ML: 0.124 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.271 / ESU R Free: 0.197 / 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: 76.67 Å2 / Biso mean: 17.951 Å2 / Biso min: 1.5 Å2
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Refinement step | Cycle: final / Resolution: 2.21→42.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.21→2.267 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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