+Open data
-Basic information
Entry | Database: PDB / ID: 1b8d | ||||||
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Title | CRYSTAL STRUCTURE OF A PHYCOUROBILIN-CONTAINING PHYCOERYTHRIN | ||||||
Components | (PROTEIN (RHODOPHYTAN PHYCOERYTHRIN ...) x 3 | ||||||
Keywords | PHOTOSYNTHESIS / LIGHT-HARVESTING COMPLEX / RED ALGAE / PHYCOBILIPROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Griffithsia monilis (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Ritter, S. / Hiller, R.G. / Wrench, P.M. / Welte, W. / Diederichs, K. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 1999 Title: Crystal structure of a phycourobilin-containing phycoerythrin at 1.90-A resolution. Authors: Ritter, S. / Hiller, R.G. / Wrench, P.M. / Welte, W. / Diederichs, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1b8d.cif.gz | 193.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b8d.ent.gz | 156 KB | Display | PDB format |
PDBx/mmJSON format | 1b8d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1b8d_validation.pdf.gz | 3.6 MB | Display | wwPDB validaton report |
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Full document | 1b8d_full_validation.pdf.gz | 3.5 MB | Display | |
Data in XML | 1b8d_validation.xml.gz | 34.9 KB | Display | |
Data in CIF | 1b8d_validation.cif.gz | 46.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b8/1b8d ftp://data.pdbj.org/pub/pdb/validation_reports/b8/1b8d | HTTPS FTP |
-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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS oper:
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-Components
-PROTEIN (RHODOPHYTAN PHYCOERYTHRIN ... , 3 types, 5 molecules AKBLG
#1: Protein | Mass: 17687.834 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: THE PHYCOBILISOMES ARE LOCATED ON THE STROMAL SIDE OF THE THYLAKOID MEMBRANES. Source: (natural) Griffithsia monilis (eukaryote) / Organelle: RHODOPLAST / References: UniProt: O36005 #2: Protein | Mass: 18511.941 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: THE PHYCOBILISOMES ARE LOCATED ON THE STROMAL SIDE OF THE THYLAKOID MEMBRANES. Source: (natural) Griffithsia monilis (eukaryote) / Organelle: RHODOPLAST / References: UniProt: O36004 #3: Protein/peptide | | Mass: 656.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Griffithsia monilis (eukaryote) / Organelle: RHODOPLAST |
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-Non-polymers , 3 types, 343 molecules
#4: Chemical | ChemComp-PEB / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 51 % |
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Crystal grow | pH: 7.5 Details: 700MM SODIUM ACETATE,5MM KCL,100MM IMIDAZOLE, PH 7.5 AT 17C |
Crystal grow | *PLUS Method: otherDetails: .refer to Ritter, S., (1997) Protein Peptide Lett., 4, 69. |
-Data collection
Diffraction | Mean temperature: 289 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.92 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1993 |
Radiation | Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→15 Å / Num. obs: 67598 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.059 |
Reflection shell | Resolution: 1.82→2 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.313 / % possible all: 92 |
Reflection | *PLUS % possible obs: 96.8 % / Num. measured all: 131195 |
Reflection shell | *PLUS % possible obs: 92 % / Num. unique obs: 15857 / Num. measured obs: 28679 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CPC Resolution: 1.9→100 Å / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: INDIVIDUAL B-FAC REFINEMENT
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Displacement parameters | Biso mean: 22.15 Å2
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Refine analyze | Luzzati coordinate error obs: 0.27 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→100 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Weight Biso : 2 / Weight position: 1
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LS refinement shell | Resolution: 1.9→1.97 Å / Total num. of bins used: 10 /
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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