+Open data
-Basic information
Entry | Database: PDB / ID: 2qdo | ||||||
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Title | NblA protein from T. vulcanus | ||||||
Components | NblA protein | ||||||
Keywords | PHOTOSYNTHESIS / Phycobilisome / nutrient starvation / bleaching | ||||||
Function / homology | Phycobilisome degradation protein NblA / Phycobilisome degradation protein NblA / Phycobilisome degradation protein NblA superfamily / Phycobilisome degradation protein nblA / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / NblA Function and homology information | ||||||
Biological species | Thermosynechococcus vulcanus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Dines, M. / Adir, N. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Structural, Functional, and Mutational Analysis of the NblA Protein Provides Insight into Possible Modes of Interaction with the Phycobilisome Authors: Dines, M. / Sendersky, E. / David, L. / Schwarz, R. / Adir, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qdo.cif.gz | 51.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qdo.ent.gz | 38.8 KB | Display | PDB format |
PDBx/mmJSON format | 2qdo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2qdo_validation.pdf.gz | 449.1 KB | Display | wwPDB validaton report |
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Full document | 2qdo_full_validation.pdf.gz | 460.2 KB | Display | |
Data in XML | 2qdo_validation.xml.gz | 11 KB | Display | |
Data in CIF | 2qdo_validation.cif.gz | 14.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qd/2qdo ftp://data.pdbj.org/pub/pdb/validation_reports/qd/2qdo | HTTPS FTP |
-Related structure data
Related structure data | 2q8vSC 3cs5C 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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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 6347.477 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermosynechococcus vulcanus (bacteria) Gene: nbla / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / References: UniProt: A7LBW5*PLUS #2: 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: 2.91 Å3/Da / Density % sol: 57.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 25% ethylene glycol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→47 Å / Num. all: 9900 / Num. obs: 9900 / % possible obs: 96.7 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 19.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2Q8V Resolution: 2.5→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 41.9 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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