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Yorodumi- PDB-4cbe: Crystal structure of complement factors H and FHL-1 binding prote... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cbe | ||||||
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Title | Crystal structure of complement factors H and FHL-1 binding protein BBH06 or CRASP-2 from Borrelia burgdorferi (Native) | ||||||
Components | COMPLEMENT REGULATOR-ACQUIRING SURFACE PROTEIN 2 (CRASP-2) | ||||||
Keywords | CELL ADHESION / LIPOPROTEIN / OUTER SURFACE LIPOPROTEIN | ||||||
Function / homology | Four Helix Bundle (Hemerythrin (Met), subunit A) - #1640 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Prokaryotic membrane lipoprotein lipid attachment site profile. / Up-down Bundle / Mainly Alpha / Complement regulator-acquiring surface protein 2 (CRASP-2) Function and homology information | ||||||
Biological species | BORRELIA BURGDORFERI (Lyme disease spirochete) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å | ||||||
Authors | Brangulis, K. / Petrovskis, I. / Kazaks, A. / Ranka, R. / Tars, K. | ||||||
Citation | Journal: FEBS J. / Year: 2014 Title: Structural Characterization of Cspz, a Complement Regulator Factor H and Fhl-1 Binding Protein from Borrelia Burgdorferi. Authors: Brangulis, K. / Petrovskis, I. / Kazaks, A. / Bogans, J. / Otikovs, M. / Jaudzems, K. / Ranka, R. / Tars, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cbe.cif.gz | 56.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cbe.ent.gz | 41 KB | Display | PDB format |
PDBx/mmJSON format | 4cbe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cb/4cbe ftp://data.pdbj.org/pub/pdb/validation_reports/cb/4cbe | HTTPS FTP |
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-Related structure data
Related structure data | 4bg0SC 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: 25052.602 Da / Num. of mol.: 1 / Fragment: RESIDUES 23-236 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BORRELIA BURGDORFERI (Lyme disease spirochete) Strain: B31 / Plasmid: PETM-11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O50665 |
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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: 1.96 Å3/Da / Density % sol: 37 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 0.2M SODIUM ACETATE, 0.1M TRIS PH 8.5, 30% PEG 2000MME |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 19, 2013 / Details: RH-COATED TOROIDAL SI MIRROR |
Radiation | Monochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→33.22 Å / Num. obs: 19733 / % possible obs: 99.8 % / Observed criterion σ(I): 3.6 / Redundancy: 3.6 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 1.77→1.87 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 6.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4BG0 Resolution: 1.83→26.55 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.269 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: 23.763 Å2
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Refinement step | Cycle: LAST / Resolution: 1.83→26.55 Å
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Refine LS restraints |
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