+Open data
-Basic information
Entry | Database: PDB / ID: 3cka | ||||||
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Title | The crystal structure of OspA mutant | ||||||
Components | Outer surface protein A | ||||||
Keywords | MEMBRANE PROTEIN / beta-sheet | ||||||
Function / homology | Outer surface lipoprotein, Borrelia / Outer surface lipoprotein domain superfamily / Borrelia lipoprotein / cell outer membrane / Prokaryotic membrane lipoprotein lipid attachment site profile. / metal ion binding / Outer Surface Protein A / Outer surface protein A / Outer surface protein A Function and homology information | ||||||
Biological species | Borreliella burgdorferi (Lyme disease spirochete) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Makabe, K. / Biancalana, M. / Terechko, V. / Koide, S. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Minimalist design of water-soluble cross-{beta} architecture. Authors: Biancalana, M. / Makabe, K. / Koide, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cka.cif.gz | 147.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cka.ent.gz | 113.9 KB | Display | PDB format |
PDBx/mmJSON format | 3cka.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ck/3cka ftp://data.pdbj.org/pub/pdb/validation_reports/ck/3cka | HTTPS FTP |
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-Related structure data
Related structure data | 3eexC 2oy7S 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: 34692.629 Da / Num. of mol.: 2 Mutation: ...Mutation: E37S,E45S,K46S,K48A,K60A,K64S,K83A,E104S,K107S,E123Y,K125L,V132L,E134F,I136Y,K308S,E309S,K323S,E37S,E45S,K46S,K48A,K60A,K64S,K83A,E104S,K107S,E123Y,K125L,V132L,E134F,I136Y,K308S,E309S,K323S,E37S,E45S,K46S,K48A,K60A,K64S,K83A,E104S,K107S,E123Y,K125L,V132L,E134F,I136Y,K308S,E309S,K323S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Borreliella burgdorferi (Lyme disease spirochete) Gene: ospA / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: D2Y4L7, UniProt: Q45040, UniProt: D0VWU8*PLUS #2: Chemical | ChemComp-1PE / #3: Water | ChemComp-HOH / | Sequence details | THERE IS AN INSERTION BETWEEN SEQUENCE DATABASE REFERENCE RESIDUES 141 AND 142. THE SEQUENCE OF THE ...THERE IS AN INSERTION BETWEEN SEQUENCE DATABASE REFERENCE RESIDUES 141 AND 142. THE SEQUENCE OF THE INSERTION IS KSSTYELFNE | |
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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: 2.41 Å3/Da / Density % sol: 48.94 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 30% PEG400, 0.1M Tris-HCl, 10mg/ml protein with 4mM Thioflavin-T, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.95373 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 6, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95373 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / Num. obs: 82033 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 22.2 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2.5 / Num. unique all: 8124 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2OY7 Resolution: 1.65→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.799 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.106 / ESU R Free: 0.106 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.523 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.678 Å / Total num. of bins used: 20
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