+Open data
-Basic information
Entry | Database: PDB / ID: 4ggt | ||||||
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Title | Structure of apo Bradavidin2 (Form B) | ||||||
Components | Bradavidin 2 | ||||||
Keywords | BIOTIN BINDING PROTEIN / bradavidin / avidin / oligomeric state / streptavidin / high affinity systems / lipocalin fold / beta barrel | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bradyrhizobium japonicum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.693 Å | ||||||
Authors | Livnah, O. / Meir, A. | ||||||
Citation | Journal: Protein Sci. / Year: 2013 Title: The highly dynamic oligomeric structure of bradavidin II is unique among avidin proteins. Authors: Leppiniemi, J. / Meir, A. / Kahkonen, N. / Kukkurainen, S. / Maatta, J.A. / Ojanen, M. / Janis, J. / Kulomaa, M.S. / Livnah, O. / Hytonen, V.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ggt.cif.gz | 57.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ggt.ent.gz | 41.2 KB | Display | PDB format |
PDBx/mmJSON format | 4ggt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gg/4ggt ftp://data.pdbj.org/pub/pdb/validation_reports/gg/4ggt | HTTPS FTP |
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-Related structure data
Related structure data | 4ggrC 4ggzC 3ew1S C: citing same article (ref.) 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 12581.157 Da / Num. of mol.: 2 / Fragment: UNP residues 19-130 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bradyrhizobium japonicum (bacteria) / Strain: USDA 110 / Gene: bll1558 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-AI / References: UniProt: Q89U61 #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: 2.48 Å3/Da / Density % sol: 50.4 % |
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Crystal grow | Temperature: 293 K / Method: microbatch / pH: 3 Details: 1 uL drop of 3.4 mg/mL protein in 0.5 M acetic acid, pH 3.0, with 0.12 M magnesium formate, diffraction parameters improved with later addition of 0.1 M sodium bromide, MICROBATCH, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 30, 2011 |
Radiation | Monochromator: channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.693→50 Å / Num. all: 23010 / Num. obs: 23010 / % possible obs: 86 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3EW1 Resolution: 1.693→40.66 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.923 / SU B: 2.34 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.135 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.69 Å2
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Refinement step | Cycle: LAST / Resolution: 1.693→40.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.693→1.737 Å / Total num. of bins used: 20
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