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- PDB-6yx7: The high resolution structure of allophycocyanin from cyanobacter... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6yx7 | ||||||||||||
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Title | The high resolution structure of allophycocyanin from cyanobacterium Nostoc sp. WR13, the P21212 crystal form. | ||||||||||||
![]() | (Allophycocyanin ...) x 2 | ||||||||||||
![]() | PHOTOSYNTHESIS / Allophycocyanin crystal structure Phycobilisome Phycobiliproteins Phycocyanobilin chromophore Light harvesting complex Cyanobacterium Nostoc sp. WR13 | ||||||||||||
Function / homology | ![]() phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Patel, H.M. / Roszak, A.W. / Madamwar, D. / Cogdell, R.J. | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: The high resolution structure of allophycocyanin from cyanobacterium Nostoc sp. WR13 Authors: Patel, H.M. / Roszak, A.W. / Madamwar, D. / Cogdell, R.J. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 887.3 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6yx8C ![]() 1b33S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS ensembles :
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Components
-Allophycocyanin ... , 2 types, 12 molecules AAACCCEEEGGGIIIKKKBBBDDDFFFHHHJJJLLL
#1: Protein | Mass: 17007.270 Da / Num. of mol.: 6 / Source method: isolated from a natural source Details: THERE IS ONE CHROMOPHORE MOLECULE, PHYCOCYANOBILIN (LIGAND ID: CYC), BOUND COVALENTLY TO ALLOPHYCOCYANIN ALPHA SUBUNIT RESIDUE CYS80; The N-terminal Methionine present in the gene sequence ...Details: THERE IS ONE CHROMOPHORE MOLECULE, PHYCOCYANOBILIN (LIGAND ID: CYC), BOUND COVALENTLY TO ALLOPHYCOCYANIN ALPHA SUBUNIT RESIDUE CYS80; The N-terminal Methionine present in the gene sequence was post-translationally removed and is not present in the crystal structure Source: (natural) ![]() Plasmid details: From the desert Rann of Kachchh (RoK), Gujarat, India References: UniProt: A0A4Y5PW22 #2: Protein | Mass: 17340.707 Da / Num. of mol.: 6 / Source method: isolated from a natural source Details: THERE IS ONE CHROMOPHORE MOLECULE, PHYCOCYANOBILIN (LIGAND ID: CYC), BOUND COVALENTLY TO ALLOPHYCOCYANIN BETA SUBUNIT RESIDUE CYS81 Source: (natural) ![]() Plasmid details: From the desert Rann of Kachchh (RoK), Gujarat, India References: UniProt: A0A4Y5PW23 |
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-Non-polymers , 15 types, 3258 molecules ![](data/chem/img/CYC.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/LYS.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/P6G.gif)
![](data/chem/img/GLU.gif)
![](data/chem/img/GLY.gif)
![](data/chem/img/ALA.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/DSN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/LYS.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/P6G.gif)
![](data/chem/img/GLU.gif)
![](data/chem/img/GLY.gif)
![](data/chem/img/ALA.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/DSN.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-CYC / #4: Chemical | ChemComp-PG4 / #5: Chemical | #6: Chemical | ChemComp-MPD / ( #7: Chemical | ChemComp-1PE / | #8: Chemical | ChemComp-PEG / #9: Chemical | ChemComp-EDO / #10: Chemical | ChemComp-P6G / | #11: Chemical | #12: Chemical | ChemComp-GLY / | #13: Chemical | ChemComp-ALA / | #14: Chemical | ChemComp-MRD / ( | #15: Chemical | #16: Chemical | #17: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.3 % / Description: Blue color plates with orthorhombic morphology |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Morpheus screen condition H12: Precipitant mix 4: 25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350; Buffer system 3: 1.0M Tris (base); bicine, pH 8.5 Additives: amino acids: 0.2M Gly, DL-Ala, DL-Ser, DL-Glu, DL-Lys |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 29, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97932 Å / Relative weight: 1 |
Reflection | Resolution: 1.419→106.372 Å / Num. obs: 383047 / % possible obs: 96.1 % / Redundancy: 8.7 % / Biso Wilson estimate: 19.64 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.027 / Rrim(I) all: 0.082 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 1.419→1.503 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.22 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 19080 / CC1/2: 0.623 / Rpim(I) all: 0.478 / Rrim(I) all: 1.313 / % possible all: 61.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1B33 Resolution: 1.419→106.372 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.972 / WRfactor Rfree: 0.178 / WRfactor Rwork: 0.127 / SU B: 3.366 / SU ML: 0.052 / Average fsc free: 0.9458 / Average fsc work: 0.9574 / Cross valid method: FREE R-VALUE / ESU R: 0.061 / ESU R Free: 0.061 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.715 Å2
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Refinement step | Cycle: LAST / Resolution: 1.419→106.372 Å
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Refine LS restraints |
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