+Open data
-Basic information
Entry | Database: PDB / ID: 2q8v | ||||||
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Title | NblA protein from T. vulcanus crystallized with urea | ||||||
Components | NblA protein | ||||||
Keywords | PROTEIN BINDING / Phycobilisome / nutrient starvation / disassembly / 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 / UREA / NblA Function and homology information | ||||||
Biological species | Thermosynechococcus vulcanus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD/Molecular Replacement / Resolution: 2.5 Å | ||||||
Authors | Adir, N. / Dines, M. | ||||||
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. #1: Journal: J.Struct.Biol. / Year: 2007 Title: Crystallization of sparingly soluble stress-related proteins from cyanobacteria by controlled urea solublization Authors: Dines, M. / Sendersky, E. / 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 | 2q8v.cif.gz | 31.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2q8v.ent.gz | 22.5 KB | Display | PDB format |
PDBx/mmJSON format | 2q8v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2q8v_validation.pdf.gz | 443.9 KB | Display | wwPDB validaton report |
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Full document | 2q8v_full_validation.pdf.gz | 446.7 KB | Display | |
Data in XML | 2q8v_validation.xml.gz | 6.8 KB | Display | |
Data in CIF | 2q8v_validation.cif.gz | 8.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q8/2q8v ftp://data.pdbj.org/pub/pdb/validation_reports/q8/2q8v | HTTPS FTP |
-Related structure data
Related structure data | 2qdoC 3cs5C 1ojhS 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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Unit cell |
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-Components
#1: Protein | Mass: 7467.691 Da / Num. of mol.: 2 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: Chemical | #3: 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: 2.7 Å3/Da / Density % sol: 54.49 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 25% elthelene glycol, 2M Urea, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction |
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Diffraction source |
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Detector | Type: ADSC QUANTUM 4 / Detector: CCD | |||||||||||||||
Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.5→50 Å / Num. obs: 6108 / % possible obs: 99.8 % / Observed criterion σ(I): 2.5 / Redundancy: 6.2 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 19.1 | |||||||||||||||
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 4.4 / Num. unique all: 849 / Rsym value: 0.358 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD/Molecular Replacement Starting model: 1OJH Resolution: 2.5→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 36.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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Refine LS restraints |
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