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- PDB-1p4p: Outer Surface Protein B of B. burgdorferi: crystal structure of t... -
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Open data
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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 | ||||||
![]() | Outer surface protein B | ||||||
![]() | MEMBRANE PROTEIN / INTERMOLECULAR BETA SHEET / EXTENDED BETA SHEET | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Becker, M. / Bunikis, J. / Lade, B.D. / Dunn, J.J. / Barbour, A.G. / Lawson, C.L. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 41.2 KB | Display | ![]() |
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PDB format | ![]() | 28.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 417.1 KB | Display | ![]() |
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Full document | ![]() | 420 KB | Display | |
Data in XML | ![]() | 9 KB | Display | |
Data in CIF | ![]() | 11.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1rjlC ![]() 1ospS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() Gene: OSPB / Plasmid: pET9c / Production host: ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() | |||||||||
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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