+Open data
-Basic information
Entry | Database: PDB / ID: 4r0o | ||||||
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Title | Crystal structure of PEGylated plastocyanin at 4.2 A resolution | ||||||
Components | Plastocyanin | ||||||
Keywords | ELECTRON TRANSPORT / PEGylation | ||||||
Function / homology | Function and homology information plasma membrane-derived thylakoid membrane / electron transfer activity / copper ion binding Similarity search - Function | ||||||
Biological species | Phormidium laminosum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.2 Å | ||||||
Authors | Cattani, G. / Vogeley, L. / Crowley, P.B. | ||||||
Citation | Journal: NAT.CHEM. / Year: 2015 Title: Structure of a PEGylated protein reveals a highly porous double-helical assembly. Authors: Cattani, G. / Vogeley, L. / Crowley, P.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4r0o.cif.gz | 93.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4r0o.ent.gz | 71.7 KB | Display | PDB format |
PDBx/mmJSON format | 4r0o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r0/4r0o ftp://data.pdbj.org/pub/pdb/validation_reports/r0/4r0o | HTTPS FTP |
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-Related structure data
Related structure data | 2w88S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 11551.052 Da / Num. of mol.: 4 / Fragment: UNP residues 35-139 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Phormidium laminosum (bacteria) / Gene: petE / Production host: Escherichia coli (E. coli) / References: UniProt: Q51883 #2: Chemical | ChemComp-CU / #3: Chemical | ChemComp-LCY / |
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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: 6.28 Å3/Da / Density % sol: 80.42 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: 48 % AMMONIUM SULPHATE, 30 mM POTASSIUM FERRICYANIDE, 100 mM SODIUM ACETATE, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 13, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 4.2→44.47 Å / Num. all: 9100 / Num. obs: 9064 / % possible obs: 99.6 % / Redundancy: 5.6 % / Biso Wilson estimate: 174.864 Å2 / Rmerge(I) obs: 0.35 / Rsym value: 0.379 / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 4.2→4.31 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.01062 / Mean I/σ(I) obs: 1.7 / Num. unique all: 662 / Rsym value: 0.01152 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2w88 Resolution: 4.2→43.035 Å / SU ML: 0.58 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.86 / 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 mean: 121.577 Å2
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Refinement step | Cycle: LAST / Resolution: 4.2→43.035 Å
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Refine LS restraints |
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LS refinement shell |
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