+Open data
-Basic information
Entry | Database: PDB / ID: 2vjh | ||||||
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Title | The structure of Phycoerythrin from Gloeobacter violaceus | ||||||
Components |
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Keywords | PHOTOSYNTHESIS / LIGHT-HARVESTING | ||||||
Function / homology | Function and homology information | ||||||
Biological species | GLOEOBACTER VIOLACEUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Murray, J.W. / Benson, S. / Nield, J. / Barber, J. | ||||||
Citation | Journal: To be Published Title: The Structures of the Phycobiliproteins of Gloeobacter Violaceus Authors: Murray, J.W. / Benson, S. / Nield, J. / Barber, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vjh.cif.gz | 160.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vjh.ent.gz | 128.8 KB | Display | PDB format |
PDBx/mmJSON format | 2vjh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vjh_validation.pdf.gz | 3.5 MB | Display | wwPDB validaton report |
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Full document | 2vjh_full_validation.pdf.gz | 3.6 MB | Display | |
Data in XML | 2vjh_validation.xml.gz | 39.2 KB | Display | |
Data in CIF | 2vjh_validation.cif.gz | 53.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vj/2vjh ftp://data.pdbj.org/pub/pdb/validation_reports/vj/2vjh | HTTPS FTP |
-Related structure data
Related structure data | 2vjrC 2vjtC 2vmlC 1b8dS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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-Components
#1: Protein | Mass: 17679.016 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PASTEUR CULTURE COLLECTION / Source: (natural) GLOEOBACTER VIOLACEUS (bacteria) / Strain: PCC7421 / References: UniProt: Q7NLD7 #2: Protein | Mass: 18458.176 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PASTEUR CULTURE COLLECTION / Source: (natural) GLOEOBACTER VIOLACEUS (bacteria) / Strain: PCC7421 / References: UniProt: Q7NLD6 #3: Chemical | ChemComp-PEB / #4: Chemical | #5: 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: 2 Å3/Da / Density % sol: 40 % / Description: NONE |
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Crystal grow | Details: 10% W/V PEG 8K, 0.33 M SODIUM CACODYLATE, 0.67 M MAGNESIUM CHLORIDE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.283 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 8, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.283 Å / Relative weight: 1 |
Reflection | Resolution: 2.19→44.99 Å / Num. obs: 64149 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 14.06 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 19.53 |
Reflection shell | Resolution: 2.19→2.21 Å / Redundancy: 9.23 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 4.28 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1B8D Resolution: 2.2→43.23 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.716 / SU ML: 0.079 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→43.23 Å
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Refine LS restraints |
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