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Yorodumi- PDB-1b33: STRUCTURE OF LIGHT HARVESTING COMPLEX OF ALLOPHYCOCYANIN ALPHA AN... -
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-Basic information
Entry | Database: PDB / ID: 1b33 | ||||||
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Title | STRUCTURE OF LIGHT HARVESTING COMPLEX OF ALLOPHYCOCYANIN ALPHA AND BETA CHAINS/CORE-LINKER COMPLEX AP*LC7.8 | ||||||
Components |
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Keywords | PHOTOSYNTHESIS / LIGHT-HARVESTING PROTEIN / CYANOBACTERIA / ALLOPHYCOCYANIN / LINKER POLYPEPTIDES / COMPLEX STRUCTURE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Mastigocladus laminosus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Reuter, W. / Wiegand, G. / Huber, R. / Than, M.E. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1999 Title: Structural analysis at 2.2 A of orthorhombic crystals presents the asymmetry of the allophycocyanin-linker complex, AP.LC7.8, from phycobilisomes of Mastigocladus laminosus. Authors: Reuter, W. / Wiegand, G. / Huber, R. / Than, M.E. #1: Journal: J.Mol.Biol. / Year: 1995 Title: Isolation, Crystallization, Crystal Structure Analysis and Refinement of Allophycocyanin from the Cyanobacterium Spirulina Platensis at 2.3 A Resolution Authors: Brejc, K. / Ficner, R. / Huber, R. / Steinbacher, S. #2: Journal: Hoppe-Seyler's Z.Physiol.Chem. / Year: 1984 Title: Minor Polypeptides from the Cyanobacterium Mastigocladus Laminosus Authors: Fueglistaller, P. / Ruembli, R. / Suter, F. / Zuber, H. #3: Journal: Hoppe-Seyler's Z.Physiol.Chem. / Year: 1981 Title: The Complete Amino Acid Sequence of Both Subunits of Allophycocyanin, a Light Harvesting Protein-Pigment Complex from the Cyanobacterium Mastigocladus Laminosus Authors: Sidler, W. / Gysi, J. / Isker, E. / Zuber, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1b33.cif.gz | 434.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b33.ent.gz | 356.2 KB | Display | PDB format |
PDBx/mmJSON format | 1b33.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1b33_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1b33_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 1b33_validation.xml.gz | 51.8 KB | Display | |
Data in CIF | 1b33_validation.cif.gz | 75.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b3/1b33 ftp://data.pdbj.org/pub/pdb/validation_reports/b3/1b33 | HTTPS FTP |
-Related structure data
Related structure data | 1allS 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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-Components
-ALLOPHYCOCYANIN, ... , 2 types, 12 molecules ACEHJLBDFIKM
#1: Protein | Mass: 17138.398 Da / Num. of mol.: 6 / Fragment: ALPHA CHAINS / Source method: isolated from a natural source Details: LONG TIME LABORATORY CULTURE, ADAPTED TO LOW TEMPERATURE Source: (natural) Mastigocladus laminosus (bacteria) / Cell line: PCC 7603 / Cellular location: CYTOPLASM, PHYCOBILISOME CORE / References: UniProt: P00315 #2: Protein | Mass: 17403.822 Da / Num. of mol.: 6 / Fragment: BETA CHAINS / Source method: isolated from a natural source Details: LONG TIME LABORATORY CULTURE, ADAPTED TO LOW TEMPERATURE Source: (natural) Mastigocladus laminosus (bacteria) / Cell line: PCC 7603 / Cellular location: CYTOPLASM, PHYCOBILISOME CORE / References: UniProt: P00318 |
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-Protein , 1 types, 2 molecules NO
#3: Protein | Mass: 7753.017 Da / Num. of mol.: 2 / Fragment: PEPTIDE LINKER / Source method: isolated from a natural source Details: LONG TIME LABORATORY CULTURE, ADAPTED TO LOW TEMPERATURE Source: (natural) Mastigocladus laminosus (bacteria) / Cell line: PCC 7603 / Cellular location: CYTOPLASM, PHYCOBILISOME CORE / References: UniProt: P20116 |
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-Non-polymers , 4 types, 1360 molecules
#4: Chemical | #5: Chemical | ChemComp-CYC / #6: Chemical | ChemComp-BO4 / #7: Water | ChemComp-HOH / | |
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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: 4.07 Å3/Da / Density % sol: 70 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.9 / Details: pH 7.9 | |||||||||||||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 27 ℃ / Method: vapor diffusion, hanging 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: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.06 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRROR |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.06 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→25 Å / Num. obs: 180426 / % possible obs: 96.6 % / Redundancy: 3.5 % / Biso Wilson estimate: 36.77 Å2 / Rsym value: 0.069 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.318 / % possible all: 96.6 |
Reflection | *PLUS Num. measured all: 637968 / Rmerge(I) obs: 0.069 |
Reflection shell | *PLUS % possible obs: 96.6 % / Rmerge(I) obs: 0.318 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ALL Resolution: 2.3→25 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0 Details: OCCUPANCY AND B-FACTOR ARE SET TO ZERO FOR ALL ATOMS, THAT ARE NOT DEFINED IN THE FINAL 2FO-FC ELECTRON DENSITY.
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Displacement parameters | Biso mean: 34.04 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.24 Å / Total num. of bins used: 20
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 25 Å / σ(F): 0 / % reflection Rfree: 4.82 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.3074 |