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- PDB-1n5b: Crystal Structure Of The Yersinia enterocolitica Molecular Chaper... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1n5b | |||||||||
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Title | Crystal Structure Of The Yersinia enterocolitica Molecular Chaperone Syce | |||||||||
![]() | YOPE regulator | |||||||||
![]() | CHAPERONE / yersinia enterocolitica / molecular chaperone / type III secretion system | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Trame, C.B. / McKay, D.B. | |||||||||
![]() | ![]() Title: Structure of the Yersinia enterocolitica molecular-chaperone protein SycE. Authors: Trame, C.B. / McKay, D.B. #1: ![]() Title: Structure of the Yersinia Type III Secretory System Chaperone Syce Authors: Birtalan, S. / Ghosh, P. #2: ![]() Title: Three-Dimensional Structure of the Type III Secretion Chaperone SycE from Yersinia Pestis Authors: Evdokimov, A.G. / Tropea, J.E. / Routzahn, K.M. / Waugh, D.S. #3: ![]() Title: Three-Dimensional Secretion Signals in Chaperone-Effector Complexes of Bacterial Pathogens Authors: Birtalan, S.C. / Phillips, R.M. / Ghosh, P. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 108.7 KB | Display | ![]() |
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PDB format | ![]() | 85.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453.2 KB | Display | ![]() |
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Full document | ![]() | 465.4 KB | Display | |
Data in XML | ![]() | 21.2 KB | Display | |
Data in CIF | ![]() | 28.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1k6zS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Details | there are 4 molecules in AU, packed as 2 dimers with an ncs translation peak in the native patterson (0.5,~0.,0.5) |
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Components
#1: Protein | Mass: 14839.753 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 42.98 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.7 Details: PEG 400, ammonium sulphate, sodium chloride, hepes, TCEP, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 27, 2002 Details: vertical focusing flat mirror, single crystal Si(111) bent monochromator (horizontal focussing) |
Radiation | Monochromator: horizontally focusing bent Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→45.72 Å / Num. obs: 34752 / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.4 % / Biso Wilson estimate: 21.7 Å2 / Rmerge(I) obs: 0.037 / Rsym value: 0.037 / Net I/σ(I): 30.6 |
Reflection shell | Resolution: 1.98→2.01 Å / Redundancy: 4 % / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 5 / Rsym value: 0.235 / % possible all: 89.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1K6Z Resolution: 2→29.54 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1519681.15 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.8009 Å2 / ksol: 0.357917 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→29.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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