+Open data
-Basic information
Entry | Database: PDB / ID: 2w88 | ||||||
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Title | Plastocyanin variant with N-terminal Methionine - open structure | ||||||
Components | PLASTOCYANIN | ||||||
Keywords | ELECTRON TRANSPORT / PROTEIN INTERACTIONS / TRANSPORT / CUPREDOXIN / SELF-ASSEMBLY / METAL-BINDING | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.89 Å | ||||||
Authors | Crowley, P.B. / Matias, P.M. / Khan, A.R. | ||||||
Citation | Journal: Chemistry / Year: 2009 Title: Metal-Mediated Self-Assembly of a Beta-Sandwich Protein. Authors: Crowley, P.B. / Matias, P.M. / Khan, A.R. / Roessle, M. / Svergun, D.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2w88.cif.gz | 73.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w88.ent.gz | 55 KB | Display | PDB format |
PDBx/mmJSON format | 2w88.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2w88_validation.pdf.gz | 433.1 KB | Display | wwPDB validaton report |
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Full document | 2w88_full_validation.pdf.gz | 434.2 KB | Display | |
Data in XML | 2w88_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | 2w88_validation.cif.gz | 16.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w8/2w88 ftp://data.pdbj.org/pub/pdb/validation_reports/w8/2w88 | HTTPS FTP |
-Related structure data
Related structure data | 2w8cC 3cvbS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 5 / Auth seq-ID: 0 - 105 / Label seq-ID: 1 - 106
NCS oper:
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-Components
#1: Protein | Mass: 11562.996 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PHORMIDIUM LAMINOSUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q51883 #2: Chemical | #3: Chemical | ChemComp-ZN / Sequence details | NO SIGNAL PEPTIDE PRESENT AND N-TERMINAL INSERTION OF MET0 | |
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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: 6.45 Å3/Da / Density % sol: 81 % / Description: NONE |
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Crystal grow | Details: 0.1 M ZINC ACETATE, 0.4 M SODIUM ACETATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 |
Detector | Type: RIGAKU IMAGING PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.89→47.78 Å / Num. obs: 19857 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Biso Wilson estimate: 54.38 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 4.3 |
Reflection shell | Resolution: 2.89→3.05 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 1.3 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3CVB Resolution: 2.89→110.43 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.904 / SU B: 18.96 / SU ML: 0.169 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.298 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES ARE RESIDUALS ONLY.
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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: 29.099 Å2
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Refinement step | Cycle: LAST / Resolution: 2.89→110.43 Å
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Refine LS restraints |
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