[English] 日本語
Yorodumi- PDB-2uul: Crystal structure of C-phycocyanin from Phormidium, Lyngbya spp. ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2uul | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of C-phycocyanin from Phormidium, Lyngbya spp. (Marine) and Spirulina sp. (Fresh water) shows two different ways of energy transfer between two hexamers. | ||||||
Components |
| ||||||
Keywords | ELECTRON TRANSPORT / C-PHYCOCYANIN / PHYCOBILISOME / PHOTOSYNTHESIS / CHROMOPHORE / FRESH WATER / METHYLATION / BILE PIGMENT / MARINE / LYNGBYA / SPIRULINA / TRANSPORT / PHORMIDIUM | ||||||
Function / homology | Phycocyanins / Globin-like / Orthogonal Bundle / Mainly Alpha / BILIVERDINE IX ALPHA / PHYCOCYANOBILIN Function and homology information | ||||||
Biological species | PHORMIDIUM SP. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Satyanarayana, L. / Patel, A. / Mishra, S. / K Ghosh, P. / Suresh, C.G. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of C-Phycocyanin from Phormidium, Lyngbya Spp. (Marine) and Spirulina Sp. (Fresh Water) Shows Two Different Ways of Energy Transfer between Twohexamers. Authors: Satyanarayana, L. / Patel, A. / Mishra, S. / Ghosh, P.K. / Suresh, C.G. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2005 Title: X-Ray Crystallographic Studies on C-Phycocyanins from Cyanobacteria from Different Habitats: Marine and Freshwater. Authors: Satyanarayana, L. / Suresh, C.G. / Patel, A. / Mishra, S. / Ghosh, P.K. #2: Journal: Protein Expr.Purif. / Year: 2005 Title: Purification and Charactarization of C-Phycocyanin from Cyanobacterial Species of Marine and Freshwater Habitat. Authors: Patel, A. / Mishra, S. / Pawar, R. / Ghosh, P.K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2uul.cif.gz | 739.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2uul.ent.gz | 627.1 KB | Display | PDB format |
PDBx/mmJSON format | 2uul.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uu/2uul ftp://data.pdbj.org/pub/pdb/validation_reports/uu/2uul | HTTPS FTP |
---|
-Related structure data
Related structure data | 1gh0S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
2 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 1
NCS ensembles :
|
-Components
-C-PHYCOCYANIN ALPHA ... , 2 types, 12 molecules AEGIKMOQSUWC
#1: Protein | Mass: 17318.387 Da / Num. of mol.: 11 / Source method: isolated from a natural source Details: PHYCOCYANOBILIN ATTACHED ALFA-84 CYSTEINE RESIDUE AND BETA-82 AND 153 MONOMERS Source: (natural) PHORMIDIUM SP. (bacteria) #3: Protein | | Mass: 17362.439 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: PHYCOCYANOBILIN ATTACHED ALFA-84 CYSTEINE RESIDUE AND BETA-82 AND 153 MONOMERS, RESIDUE 143 IS SER IN CHAIN C WHERE AS IT IS ALA IN OTHER CHAINS Source: (natural) PHORMIDIUM SP. (bacteria) |
---|
-C-PHYCOCYANIN BETA ... , 3 types, 12 molecules BFJLNPRTVXDH
#2: Protein | Mass: 17827.139 Da / Num. of mol.: 10 / Source method: isolated from a natural source Details: PHYCOCYANOBILIN ATTACHED ALFA-84 CYSTEINE RESIDUE AND BETA-82 AND 153 MONOMERS Source: (natural) PHORMIDIUM SP. (bacteria) #4: Protein | | Mass: 17959.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: PHYCOCYANOBILIN ATTACHED ALFA-84 CYSTEINE RESIDUE AND BETA-82 AND 153 MONOMERS, RESIDUES 9 AND 10 ARE VAL SER IN THIS CHAIN WHEREAS IT IS ALA ALA IN OTHER CHAINS Source: (natural) PHORMIDIUM SP. (bacteria) #5: Protein | | Mass: 17779.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: PHYCOCYANOBILIN ATTACHED ALFA-84 CYSTEINE RESIDUE AND BETA-82 AND 153 MONOMERS, RESIDUE 74 IS ASP IN THIS CHAIN WHERE AS IT IS TYR IN OTHER CHAINS Source: (natural) PHORMIDIUM SP. (bacteria) |
---|
-Non-polymers , 3 types, 175 molecules
#6: Chemical | ChemComp-CYC / #7: Chemical | #8: Water | ChemComp-HOH / | |
---|
-Details
Sequence details | THE SPECIES FROM WHICH THE PROTEIN HAS BEEN EXTRACTED IS CURRENTLY UNKNOWN. THIS PDB ENTRY HAS BEEN ...THE SPECIES FROM WHICH THE PROTEIN HAS BEEN EXTRACTED IS CURRENTLY UNKNOWN. THIS PDB ENTRY HAS BEEN MAPPED AGAINST ITSELF. THE ONLY KNOWN FACT IS THE GRANDPAREN |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50 % / Description: NONE |
---|---|
Crystal grow | pH: 6.5 Details: 0.01M SODIUM PHOSPHATE PH 6.5, 0.72M SOD. FORMATE, 9%PEG 1K AND 9% PEG 8K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3→40 Å / Num. obs: 82067 / % possible obs: 96.6 % / Observed criterion σ(I): 2 / Redundancy: 2.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 5.27 |
Reflection shell | Resolution: 3→3.11 Å / Rmerge(I) obs: 0.03 / Mean I/σ(I) obs: 2.46 / % possible all: 93.4 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GH0 Resolution: 3.1→25 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.85 / SU B: 19.91 / SU ML: 0.354 / Cross valid method: THROUGHOUT / ESU R Free: 0.521 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.36 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→25 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|