[English] 日本語
Yorodumi- PDB-4dp8: The 1.07 Angstrom crystal structure of reduced (CuI) poplar plast... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dp8 | ||||||
---|---|---|---|---|---|---|---|
Title | The 1.07 Angstrom crystal structure of reduced (CuI) poplar plastocyanin A at pH 4.0 | ||||||
Components | Plastocyanin A, chloroplastic | ||||||
Keywords | ELECTRON TRANSPORT / membrane / thylakoid / transit peptide / plastocyanin-like domain / copper-binding | ||||||
Function / homology | Function and homology information electron transporter, transferring electrons from cytochrome b6/f complex of photosystem II activity / chloroplast thylakoid lumen / chloroplast thylakoid membrane / copper ion binding Similarity search - Function | ||||||
Biological species | Populus nigra (black poplar) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.07 Å | ||||||
Authors | Kachalova, G.S. / Shosheva, A.H. / Bourenkov, G.P. / Donchev, A.A. / Dimitrov, M.I. / Bartunik, H.D. | ||||||
Citation | Journal: J.Inorg.Biochem. / Year: 2012 Title: Structural comparison of the poplar plastocyanin isoforms PCa and PCb sheds new light on the role of the copper site geometry in interactions with redox partners in oxygenic photosynthesis. Authors: Kachalova, G.S. / Shosheva, A.C. / Bourenkov, G.P. / Donchev, A.A. / Dimitrov, M.I. / Bartunik, H.D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4dp8.cif.gz | 61.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4dp8.ent.gz | 46.1 KB | Display | PDB format |
PDBx/mmJSON format | 4dp8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dp/4dp8 ftp://data.pdbj.org/pub/pdb/validation_reports/dp/4dp8 | HTTPS FTP |
---|
-Related structure data
Related structure data | 4dp0C 4dp1C 4dp2C 4dp4C 4dp5C 4dp6C 4dp7C 4dp9C 4dpaC 4dpbC 4dpcC 1plcS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 10493.607 Da / Num. of mol.: 1 / Fragment: UNP residues 70-168 / Source method: isolated from a natural source / Source: (natural) Populus nigra (black poplar) / Organelle: chloroplast / Strain: cv. Italica / Tissue: leaf / References: UniProt: P00299 |
---|---|
#2: Chemical | ChemComp-CU1 / |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.83 Å3/Da / Density % sol: 32.76 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 2.6 M ammonium sulfate, 0.1 M sodium phosphate buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 5, 2002 / Details: MIRRORS |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 1.07→15.85 Å / Num. all: 34778 / Num. obs: 33658 / % possible obs: 96.8 % / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Biso Wilson estimate: 10.07 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 22.6 |
Reflection shell | Resolution: 1.07→1.09 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1717 / % possible all: 90.7 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PLC Resolution: 1.07→15.85 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.967 / SU B: 0.832 / SU ML: 0.019 / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.032 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 mean: 15.027 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.07→15.85 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.07→1.098 Å / Total num. of bins used: 20
|