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Yorodumi- PDB-1ha7: STRUCTURE OF A LIGHT-HARVESTING PHYCOBILIPROTEIN, C-PHYCOCYANIN F... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ha7 | ||||||
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Title | STRUCTURE OF A LIGHT-HARVESTING PHYCOBILIPROTEIN, C-PHYCOCYANIN FROM SPIRULINA PLATENSIS AT 2.2A RESOLUTION | ||||||
Components |
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Keywords | PHOTOSYNTHESIS / CYANOBACTERIA / LIGHT-HARVESTING PROTEIN / PIGMENT PROTEIN / PHYCOCYANOBILIN / CHROMOPHORE | ||||||
Function / homology | Function and homology information phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis Similarity search - Function | ||||||
Biological species | SPIRULINA PLATENSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Padyana, A.K. / Rajashankar, K.R. / Ramakumar, S. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2001 Title: Crystal Structure of a Light-Harvesting Protein C-Phycocyanin from Spirulina Platensis Authors: Padyana, A.K. / Bhat, V.B. / Madyastha, K.M. / Rajashankar, K.R. / Ramakumar, S. #1: Journal: Biophys.J. / Year: 1999 Title: Crystal Structure of C-Phycocyanin from Cyanidium Caldarium Provides a New Perspective on Phycobilisome Assembly Authors: Stec, B. / Troxler, R.F. / Teeter, M.M. #2: Journal: J.Mol.Biol. / Year: 1991 Title: Isolation, Crystallization, Crystal Structure Analysis and Refinement of Constitutive C-Phycocyanin from the Chromatically Adapting Cyanobacterium Fremyella Diplosiphon at 1.66 Angstrom Resolution Authors: Duerring, M. / Schmidt, G.B. / Huber, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ha7.cif.gz | 803 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ha7.ent.gz | 679.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ha7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ha/1ha7 ftp://data.pdbj.org/pub/pdb/validation_reports/ha/1ha7 | HTTPS FTP |
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-Related structure data
Related structure data | 1cpcS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | (ALPHA,BETA)*6-HEXAMER. THERE ARE TWO HEXAMERS WITH TWELVECHAINS EACH, IN THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT.THIS STRUCTURE CONTAINS 36 PHYCOCYANOBILIN CHROMOPHORESDISTRIBUTED IN TWO HEXAMERS WITH 18 EACH IN A HEXAMER. CHROMOPHORES ARE COVALENTLY ATTACHED BY THIOETHER BONDS TOCYSTEINE RESIDUES AT THREE POSITIONS IN A (ALPHA,BETA)-MONOMERAT ALPHA 84, BETA 84 AND BETA 155 POSITIONS RESPECTIVELY.SG ATOM OF CYSTEINE RESIDUE IS COVALENTLY BONDED TO CAC ATOMOF CYC (PHYCOCYANOBILIN CHROMOPHORE). |
-Components
#1: Protein | Mass: 17618.820 Da / Num. of mol.: 12 / Fragment: ALPHA-CHAIN / Source method: isolated from a natural source / Source: (natural) SPIRULINA PLATENSIS (bacteria) / Cellular location: STROMAL SURFACE, PHYCOBILISOME ROD / References: UniProt: P72509 #2: Protein | Mass: 18122.559 Da / Num. of mol.: 12 / Fragment: BETA-CHAIN / Source method: isolated from a natural source / Source: (natural) SPIRULINA PLATENSIS (bacteria) / Cellular location: STROMAL SURFACE, PHYCOBILISOME ROD / References: UniProt: P72508 #3: Chemical | ChemComp-CYC / #4: Water | ChemComp-HOH / | Sequence details | ALPHA CHAINS ARE NUMBERED 1 - 174 WITH A NUMBERING GAP. RESIDUES 143 AND 156 ARE CONSECUTIVE ...ALPHA CHAINS ARE NUMBERED 1 - 174 WITH A NUMBERING GAP. RESIDUES 143 AND 156 ARE CONSECUTIV | |
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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: 2.5 Å3/Da / Density % sol: 51 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.8 Details: 23% (W/V) PEG 6000, 10% (V/V) OF ETHANOL, 75 MM OF PHOSPHATE BUFFER (PH 6.8) | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.98 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 14, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→25 Å / Num. obs: 223480 / % possible obs: 99.3 % / Redundancy: 5.3 % / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2.2→2.28 Å / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 2.5 / % possible all: 97.8 |
Reflection | *PLUS Num. measured all: 1177344 |
Reflection shell | *PLUS Highest resolution: 2.2 Å / % possible obs: 97.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1CPC Resolution: 2.2→22.9 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 212513.6 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / ksol: 0.332493 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→22.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 25 Å / Rfactor Rfree: 0.239 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 27.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 2.28 Å / Rfactor Rfree: 0.303 / Rfactor Rwork: 0.262 / Rfactor obs: 0.262 |