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Yorodumi- PDB-2q5b: High resolution structure of Plastocyanin from Phormidium laminosum -
+Open data
-Basic information
Entry | Database: PDB / ID: 2q5b | ||||||
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Title | High resolution structure of Plastocyanin from Phormidium laminosum | ||||||
Components | Plastocyanin | ||||||
Keywords | ELECTRON TRANSPORT / Plastocyanin / Photosystem 1 | ||||||
Function / homology | Function and homology information electron transporter, transferring electrons from cytochrome b6/f complex of photosystem II activity / plasma membrane-derived thylakoid membrane / copper ion binding Similarity search - Function | ||||||
Biological species | Phormidium laminosum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Fromme, R. / Bukhman-DeRuyter, Y.S. / Grotjohann, I. / Mi, H. / Fromme, P. | ||||||
Citation | Journal: To be Published Title: Plastocyanin at high resolution from Phormidium laminosum and the double mutant D44A, D45A Authors: Bukhman-DeRuyter, Y.S. / Fromme, R. / Grotjohann, I. / Schlarb-Ridley, B. / Mi, H. / Fromme, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2q5b.cif.gz | 142 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2q5b.ent.gz | 111.3 KB | Display | PDB format |
PDBx/mmJSON format | 2q5b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q5/2q5b ftp://data.pdbj.org/pub/pdb/validation_reports/q5/2q5b | HTTPS FTP |
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-Related structure data
Related structure data | 1bawS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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5 |
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Unit cell |
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Components on special symmetry positions |
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Details | The biological unit is the monomer. |
-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 11431.800 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Phormidium laminosum (bacteria) / Gene: petE / Plasmid: pET11Pc / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q51883 |
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-Non-polymers , 5 types, 281 molecules
#2: Chemical | #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-K / #5: Chemical | ChemComp-ACT / | #6: 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: 2.34 Å3/Da / Density % sol: 47.55 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1 M NA CACODYLATE BUFFER (PH 6), 0.2 M ZN ACETATE, 15% PEG 8000 , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 28, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→42.11 Å / Num. all: 57906 / Num. obs: 57906 / % possible obs: 99.6 % / Redundancy: 9.6 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 25.4 |
Reflection shell | Resolution: 1.45→1.5 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.626 / Mean I/σ(I) obs: 2 / % possible all: 96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BAW Resolution: 1.45→9.99 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.541 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.07 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.719 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→9.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.452→1.489 Å / Total num. of bins used: 20
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