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Yorodumi- PDB-1p4p: Outer Surface Protein B of B. burgdorferi: crystal structure of t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1p4p | ||||||
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Title | Outer Surface Protein B of B. burgdorferi: crystal structure of the C-terminal fragment | ||||||
Components | Outer surface protein B | ||||||
Keywords | MEMBRANE PROTEIN / INTERMOLECULAR BETA SHEET / EXTENDED BETA SHEET | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Borrelia burgdorferi (Lyme disease spirochete) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 650 | HELIX DETERMINATION METHOD: AUTHOR |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1p4p.cif.gz | 41.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1p4p.ent.gz | 28.6 KB | Display | PDB format |
PDBx/mmJSON format | 1p4p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1p4p_validation.pdf.gz | 417.1 KB | Display | wwPDB validaton report |
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Full document | 1p4p_full_validation.pdf.gz | 420 KB | Display | |
Data in XML | 1p4p_validation.xml.gz | 9 KB | Display | |
Data in CIF | 1p4p_validation.cif.gz | 11.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p4/1p4p ftp://data.pdbj.org/pub/pdb/validation_reports/p4/1p4p | HTTPS FTP |
-Related structure data
Related structure data | 1rjlC 1ospS 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: 15653.579 Da / Num. of mol.: 1 / Fragment: OspB C-terminal fragment Source method: isolated from a genetically manipulated source Source: (gene. exp.) Borrelia burgdorferi (Lyme disease spirochete) Gene: OSPB / Plasmid: pET9c / Production host: Escherichia coli (E. coli) / Strain (production host): BL2(DE3)/pLysS / References: UniProt: P17739 |
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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: 2.02 Å3/Da / Density % sol: 39.05 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: PEG550MME, Bicine, sodium bromide, sodium citrate, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 283 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.979, 1.073 | |||||||||
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 1997 / Details: focusing mirror | |||||||||
Radiation | Monochromator: two-crystal Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2→50 Å / Num. all: 9012 / Num. obs: 8090 / % possible obs: 89.8 % / Observed criterion σ(F): -10 / Observed criterion σ(I): -10 / Redundancy: 23.7 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 34.1 | |||||||||
Reflection shell | Resolution: 2→2.03 Å / Rmerge(I) obs: 0.206 / Mean I/σ(I) obs: 12.6 / % possible all: 77.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OSP Resolution: 2→30 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Used CNS for simulated annealing, followed by conjugate gradient minimization against the maximum likelihood function. Then ran Refmac, and followed with 1 step of B-factor refinement in CNS. ...Details: Used CNS for simulated annealing, followed by conjugate gradient minimization against the maximum likelihood function. Then ran Refmac, and followed with 1 step of B-factor refinement in CNS. The loop from residue 218 to residue 221 (LYS ASP GLY LYS) is poorly ordered (is not clearly defined in the density).
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Displacement parameters | Biso mean: 32.3 Å2
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Refine analyze | Luzzati coordinate error obs: 0.247 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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