+Open data
-Basic information
Entry | Database: PDB / ID: 1ojh | ||||||
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Title | Crystal structure of NblA from PCC 7120 | ||||||
Components | NBLA | ||||||
Keywords | PROTEIN BINDING / DEGRADATION PROTEIN / PHYCOBILISOME DEGRADATION | ||||||
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 protein Function and homology information | ||||||
Biological species | ANABAENA SP. PCC 7120 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | Bienert, R. / Baier, K. / Lockau, W. / Heinemann, U. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: Crystal Structure of Nbla from Anabaena Sp. Pcc 7120, a Small Protein Playing a Key Role in Phycobilisome Degradation. Authors: Bienert, R. / Baier, K. / Volkmer, R. / Lockau, W. / Heinemann, U. #1: Journal: Fems Microbiol.Lett. / Year: 2001 Title: Expression of Two Nbla-Homologous Genes is Required for Phycobilisome Degradation in Nitrogen-Starved Synechocystis Sp. Pcc6803 Authors: Baier, K. / Nicklisch, S. / Grundner, C. / Reinecke, J. / Lockau, W. #2: Journal: Embo J. / Year: 1994 Title: A Small Polypeptide Triggers Complete Degradation of Light-Harvesting Phycobiliproteins in Nutrient-Deprived Cyanobacteria Authors: Collier, J.L. / Grossmann, A.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ojh.cif.gz | 142.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ojh.ent.gz | 123.2 KB | Display | PDB format |
PDBx/mmJSON format | 1ojh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ojh_validation.pdf.gz | 529.9 KB | Display | wwPDB validaton report |
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Full document | 1ojh_full_validation.pdf.gz | 536.6 KB | Display | |
Data in XML | 1ojh_validation.xml.gz | 24.9 KB | Display | |
Data in CIF | 1ojh_validation.cif.gz | 36.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oj/1ojh ftp://data.pdbj.org/pub/pdb/validation_reports/oj/1ojh | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
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Unit cell |
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-Components
#1: Protein | Mass: 7690.148 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ANABAENA SP. PCC 7120 (bacteria) / Plasmid: PET11A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q8YNP7 #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: 2.3 Å3/Da / Density % sol: 47 % |
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Crystal grow | pH: 8.5 Details: 100 MM TRIS/HCL PH 8.5 10% PEG2000, 100 MM MGCL2, 15% ETHYLENGLYCOL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 15, 2002 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: DOUBLE CRYSTAL, SI(111) OR SI(311) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9393 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 74292 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.8→1.97 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.8 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: SAD / Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.531 / SU ML: 0.077 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.107 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.72 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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