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- PDB-1g9u: CRYSTAL STRUCTURE OF YOPM-LEUCINE RICH EFFECTOR PROTEIN FROM YERS... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1g9u | ||||||
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Title | CRYSTAL STRUCTURE OF YOPM-LEUCINE RICH EFFECTOR PROTEIN FROM YERSINIA PESTIS | ||||||
![]() | OUTER PROTEIN YOPM | ||||||
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Function / homology | ![]() | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Evdokimov, A.G. / Anderson, D.E. / Routzahn, K.M. / Waugh, D.S. | ||||||
![]() | ![]() Title: Unusual molecular architecture of the Yersinia pestis cytotoxin YopM: a leucine-rich repeat protein with the shortest repeating unit. Authors: Evdokimov, A.G. / Anderson, D.E. / Routzahn, K.M. / Waugh, D.S. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE representing a possible biologically significant oligomerization state. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 94.1 KB | Display | ![]() |
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PDB format | ![]() | 68.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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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 | Putative biological assembly is a tetramer. |
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Components
#1: Protein | Mass: 51588.652 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
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#2: Chemical | ChemComp-ACT / ![]() #3: Chemical | #4: Chemical | ChemComp-HG / ![]() #5: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.14 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow![]() | Method: vapor diffusion, hanging drop / pH: 6 Details: 10% isopropanol 0.1 M MES, 0.2-0.4 M Ca(OAc)2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 321.0K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusionDetails: Evdokimov, A.G., (2000) Acta Crystallog., D56, 1676. | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 22, 2000 / Details: synchrotron Si monochromator + Osmic mirrors |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.32→74 Å / Num. all: 49157 / Num. obs: 39896 / % possible obs: 81 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 4 / Redundancy: 1.9 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2.32→2.45 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.2 / Num. unique all: 7609 / % possible all: 96.4 |
Reflection | *PLUS Lowest resolution: 74 Å |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: new structure Resolution: 2.35→100 Å / Isotropic thermal model: isotropic per atom / Cross valid method: random 5% throughout the refinement / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 33 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→100 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→100 Å / Rfactor Rfree error: 0.02
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 100 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor all![]() ![]() ![]() | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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