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- PDB-1r77: Crystal structure of the cell wall targeting domain of peptidylgl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1r77 | ||||||
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Title | Crystal structure of the cell wall targeting domain of peptidylglycan hydrolase ALE-1 | ||||||
![]() | Cell Wall Targeting Domain of Glycylglycine Endopeptidase ALE-1 | ||||||
![]() | HYDROLASE / SH3b Domain / Cell Wall Targeting Domain / Lysostaphin / Peptidoglycan Hydrolase / Glycylglycine Endopeptidase | ||||||
Function / homology | ![]() lysostaphin / cell wall organization / metallopeptidase activity / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lu, J.Z. / Fujiwara, T. / Komatsuzawa, H. / Sugai, M. / Sakon, J. | ||||||
![]() | ![]() Title: Cell Wall-targeting Domain of Glycylglycine Endopeptidase Distinguishes among Peptidoglycan Cross-bridges. Authors: Lu, J.Z. / Fujiwara, T. / Komatsuzawa, H. / Sugai, M. / Sakon, J. #1: ![]() Title: Purification and molecular characterization of glycylglycine endopeptidase produced by Staphylococcus capitis EPK1. Authors: Sugai, M. / Fujiwara, T. / Akiyama, T. / Ohara, M. / Komatsuzawa, H. / Inoue, S. / Suginaka, H. | ||||||
History |
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Remark 999 | SEQUENCE FLAG-tag was added to the N-terminus |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 56.5 KB | Display | ![]() |
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PDB format | ![]() | 41.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 430.7 KB | Display | ![]() |
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Full document | ![]() | 432.4 KB | Display | |
Data in XML | ![]() | 12.2 KB | Display | |
Data in CIF | ![]() | 17.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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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Unit cell |
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Components
#1: Protein | Mass: 11759.253 Da / Num. of mol.: 2 / Fragment: Cell Wall Targeting Domain / Mutation: FLAG-tag added at N-terminus 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: 2.39 Å3/Da / Density % sol: 48.58 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 3350, sodium acetate, MES pH 6.5 or HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.75→20 Å / Num. all: 23430 / Num. obs: 22012 / % possible obs: 93.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 13.5 Å2 | ||||||||||||||||||
Reflection shell | Resolution: 1.75→1.81 Å / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: N-terminus truncated SeMet MAD structure Resolution: 1.75→17.5 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 250222.27 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 53.2203 Å2 / ksol: 0.389424 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.75→17.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.86 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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