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Yorodumi- PDB-4b2f: N-terminal deletion mutant of an outer surface protein BBA73 from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4b2f | ||||||
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Title | N-terminal deletion mutant of an outer surface protein BBA73 from Borrelia burgdorferi | ||||||
Components | PUTATIVE ANTIGEN P35 | ||||||
Keywords | MEMBRANE PROTEIN / OUTER SURFACE LIPOPROTEIN | ||||||
Function / homology | Bbcrasp-1 / Bbcrasp-1 / Borrelia lipoprotein paralogus family 54/60 / Borrelia Bbcrasp-1 domain containing protein / Orthogonal Bundle / Mainly Alpha / membrane / Antigen P35 Function and homology information | ||||||
Biological species | BORRELIA BURGDORFERI (Lyme disease spirochete) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å | ||||||
Authors | Brangulis, K. / Petrovskis, I. / Kazaks, A. / Tars, K. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2013 Title: Structural Characterization of the Borrelia Burgdorferi Outer Surface Protein Bba73 Implicates Dimerization as a Functional Mechanism. Authors: Brangulis, K. / Petrovskis, I. / Kazaks, A. / Baumanis, V. / Tars, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4b2f.cif.gz | 55.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4b2f.ent.gz | 39.4 KB | Display | PDB format |
PDBx/mmJSON format | 4b2f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b2/4b2f ftp://data.pdbj.org/pub/pdb/validation_reports/b2/4b2f | HTTPS FTP |
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-Related structure data
Related structure data | 4axzSC 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: 24902.344 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DELETION MUTANT, RESIDUES 87-296 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BORRELIA BURGDORFERI (Lyme disease spirochete) Strain: B31 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O50962 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.8 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: 0.1M MES PH6.5, 18% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.0408 |
Detector | Type: MARRESEARCH MAR 165 / Detector: CCD / Date: Jul 1, 2012 / Details: MULTILAYER MIRROR |
Radiation | Monochromator: BENT SI (111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0408 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→24.2 Å / Num. obs: 21966 / % possible obs: 98.6 % / Observed criterion σ(I): 1.5 / Redundancy: 4.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 1.88→1.98 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4AXZ Resolution: 1.88→23.03 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.924 / SU B: 2.744 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.131 / 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: 23.886 Å2
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Refinement step | Cycle: LAST / Resolution: 1.88→23.03 Å
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Refine LS restraints |
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