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Yorodumi- PDB-1rjl: Structure of the complex between OspB-CT and bactericidal Fab-H6831 -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rjl | ||||||
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Title | Structure of the complex between OspB-CT and bactericidal Fab-H6831 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Beta Sheet / Antibody-Protein Complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Borrelia burgdorferi (Lyme disease spirochete) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Becker, M. / Bunikis, J. / Lade, B.D. / Dunn, J.J. / Barbour, A.G. / Lawson, C.L. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Structural Investigation of Borrelia burgdorferi OspB, a BactericidalFab Target. Authors: Becker, M. / Bunikis, J. / Lade, B.D. / Dunn, J.J. / Barbour, A.G. / Lawson, C.L. | ||||||
History |
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Remark 999 | SEQUENCE CHAINS A AND B: NO SUITABLE SEQUENCE DATABASE REFERENCE WAS FOUND AT THE TIME OF ...SEQUENCE CHAINS A AND B: NO SUITABLE SEQUENCE DATABASE REFERENCE WAS FOUND AT THE TIME OF PROCESSING. CHAIN C: THE SEQUENCE LISTED IN THE SEQRES FOR CHAIN C IS THE PORTION OF THE FOLLOWING CONSTRUCT THAT WAS CLEARLY OBSERVED IN THE DENSITY: ANKLDSKKLTRSNGTTLEYSQITDADNATKAVETLKNSIKLEGSLVVGKTTVEIK EGTVTLKREIEKDGKVKVFLNDTAGSNKKTGKWEDSTSTLTISADSKKTKDLVFL TDGTITVQQYNTAGTSLEGSASEIKNLSELKNALK THE AUTHORS DO NOT KNOW IF THE PORTION OF THE CONSTRUCT THAT WAS NOT OBSERVED IN THE DENSITY WAS MISSING DUE TO PROTEOLYSIS, OR WAS DISORDERED IN THE CRYSTAL. CHAIN D: THE AUTHORS SAW AN EXTRA BETA STRAND OF DENSITY THAT WAS NOT CONTINUOUS WITH THE MAIN BODY OF DENSITY (I.E. THERE WAS NO DENSITY FOR A CONNECTING LOOP) AND THAT DID NOT SHOW CLEAR SIDECHAIN DENSITY. THIS STRAND PRESUMABLY ARISES FROM SOME PORTION OR PORTIONS OF THE REMAINING 'UNOBSERVED' SEQUENCE ABOVE, BUT SINCE THE REGISTER WAS UNKNOWN, THE AUTHORS MODELLED IT AS A POLYALANINE STRAND, LISTED IN THE SEQRES AND COORDINATES AS UNK, UNKNOWN RESIDUE. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rjl.cif.gz | 118.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rjl.ent.gz | 91.3 KB | Display | PDB format |
PDBx/mmJSON format | 1rjl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rj/1rjl ftp://data.pdbj.org/pub/pdb/validation_reports/rj/1rjl | HTTPS FTP |
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-Related structure data
Related structure data | 1p4pC 1ospS 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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Unit cell |
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Components on special symmetry positions |
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Details | The biological assembly consists of one Fab:OspB-CT complex, which forms the asymmetric unit. |
-Components
#1: Antibody | Mass: 23218.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: BALB-C |
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#2: Antibody | Mass: 23659.381 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: BALB-C |
#3: Protein | Mass: 10310.563 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Borrelia burgdorferi (Lyme disease spirochete) Gene: OSPB, BBA16 / Plasmid: pET9c / Production host: Escherichia coli (E. coli) / Strain (production host): BL2(DE3)/pLysS / References: UniProt: P17739 |
#4: Protein/peptide | Mass: 443.539 Da / Num. of mol.: 1 / Fragment: 5-residue polyunknown fragment Source method: isolated from a genetically manipulated source Source: (gene. exp.) Borrelia burgdorferi (Lyme disease spirochete) Gene: OSPB, BBA16 / Plasmid: pET9c / Production host: Escherichia coli (E. coli) / Strain (production host): BL2(DE3)/pLysS |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal |
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Crystal grow |
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-Data collection
Diffraction | Mean temperature: 288 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.98 Å |
Detector | Type: BRANDEIS / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30.09 Å / Num. obs: 17715 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Redundancy: 7.9 % / Biso Wilson estimate: 39.3 Å2 / Limit h max: 71 / Limit h min: -71 / Limit k max: 14 / Limit k min: -71 / Limit l max: 33 / Limit l min: 0 / Observed criterion F max: 508735.16 / Observed criterion F min: 0.45 / Rmerge(I) obs: 0.078 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 2.6→2.64 Å / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 4.8 / % possible all: 87.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Fab portion of PDB ENTRY 1OSP Resolution: 2.6→30.09 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 35.2404 Å2 / ksol: 0.303959 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 98.73 Å2 / Biso mean: 39.2 Å2 / Biso min: 1.43 Å2
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Refine Biso |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→30.09 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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Xplor file |
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