[English] 日本語
Yorodumi- PDB-6s5l: Anabaena Apo-C-Terminal Domain Homolog Of The Orange Carotenoid P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6s5l | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Anabaena Apo-C-Terminal Domain Homolog Of The Orange Carotenoid Protein In Native Conditions | |||||||||
Components | All4940 protein | |||||||||
Keywords | PHOTOSYNTHESIS / OCP / orange carotenod protein / carotenoid transfer / CTDH / apoCTDH / CTT | |||||||||
Function / homology | Nuclear transport factor 2 domain / Nuclear transport factor 2 (NTF2) domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / All4940 protein Function and homology information | |||||||||
Biological species | Nostoc sp. (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | |||||||||
Authors | Harris, D. / Muzzopappa, F. / Kirilovsky, D. / Adir, N. | |||||||||
Funding support | Israel, 2items
| |||||||||
Citation | Journal: Biochim Biophys Acta Bioenerg / Year: 2020 Title: Structural dynamics in the C terminal domain homolog of orange carotenoid Protein reveals residues critical for carotenoid uptake. Authors: Harris, D. / Muzzopappa, F. / Glaser, F. / Wilson, A. / Kirilovsky, D. / Adir, N. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6s5l.cif.gz | 288.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6s5l.ent.gz | 234.7 KB | Display | PDB format |
PDBx/mmJSON format | 6s5l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6s5l_validation.pdf.gz | 501 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6s5l_full_validation.pdf.gz | 522.7 KB | Display | |
Data in XML | 6s5l_validation.xml.gz | 51.4 KB | Display | |
Data in CIF | 6s5l_validation.cif.gz | 70.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s5/6s5l ftp://data.pdbj.org/pub/pdb/validation_reports/s5/6s5l | HTTPS FTP |
-Related structure data
Related structure data | 6fejS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 15134.114 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria) Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / Gene: all4940 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YMJ3 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.23 Å3/Da / Density % sol: 61.95 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 1.26M NaH2PO4, 0.14M K2HPO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 5, 2018 |
Radiation | Monochromator: C(110) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→47.99 Å / Num. obs: 53339 / % possible obs: 99.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.036 / Rrim(I) all: 0.071 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 2.9→3.06 Å / Redundancy: 3.9 % / Num. unique obs: 7646 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6FEJ Resolution: 2.9→47.99 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.9 / SU B: 16.255 / SU ML: 0.292 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.948 / ESU R Free: 0.356 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 173.15 Å2 / Biso mean: 69.988 Å2 / Biso min: 22.43 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.9→47.99 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.9→2.975 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|