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- PDB-6u0o: Crystal structure of a peptidoglycan release complex, SagB-SpdC, ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6u0o | ||||||
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Title | Crystal structure of a peptidoglycan release complex, SagB-SpdC, in lipidic cubic phase | ||||||
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![]() | HYDROLASE / Glucosaminidase / Peptidoglycan hydrolase / CAAX protease | ||||||
Function / homology | ![]() amidase activity / membrane => GO:0016020 / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() Synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Owens, T.W. / Schaefer, K. / Kahne, D. / Walker, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure and reconstitution of a hydrolase complex that may release peptidoglycan from the membrane after polymerization. Authors: Schaefer, K. / Owens, T.W. / Page, J.E. / Santiago, M. / Kahne, D. / Walker, S. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2012 Title: Towards automated crystallographic structure refinement with phenix.refine. Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D. #2: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010 Title: PHENIX: a comprehensive Python-based system for macromolecular structure solution. Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy ...Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy / Nigel W Moriarty / Robert Oeffner / Randy J Read / David C Richardson / Jane S Richardson / Thomas C Terwilliger / Peter H Zwart / ![]() Abstract: Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many ...Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 281.2 KB | Display | ![]() |
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PDB format | ![]() | 190.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 716.6 KB | Display | ![]() |
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Full document | ![]() | 723.3 KB | Display | |
Data in XML | ![]() | 22.8 KB | Display | |
Data in CIF | ![]() | 30.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6fxpS 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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Unit cell |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 31024.703 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: N-terminal FLAG tag and linker Source: (gene. exp.) ![]() Strain: bovine RF122 / ET3-1 / Gene: lyrA, SAB2212 / Production host: ![]() ![]() |
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#2: Protein | Mass: 34086.762 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: C-terminal polyhistine tag Source: (gene. exp.) ![]() Strain: NCTC 8325 / Gene: SAOUHSC_01895 / Production host: ![]() ![]() |
-Protein/peptide , 1 types, 1 molecules D
#3: Protein/peptide | Mass: 1014.988 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others) |
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-Non-polymers , 6 types, 88 molecules ![](data/chem/img/FLC.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/OLC.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/AE3.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/OLC.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/AE3.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-FLC / | ||||
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#5: Chemical | ChemComp-PG4 / | ||||
#6: Chemical | ChemComp-OLC / ( | ||||
#7: Chemical | #8: Chemical | #9: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.23 Å3/Da / Density % sol: 61.88 % |
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Crystal grow | Temperature: 298 K / Method: lipidic cubic phase Details: 24-32% PEG400, 0.5M ammonium sulfate, 100mM sodium citrate or sodium acetate pH 4.4-5.0 (4.6 optimal), 35 mg/mL protein PH range: 4.4-5.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 13, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→46.98 Å / Num. obs: 24207 / % possible obs: 99.3 % / Redundancy: 5.8 % / Biso Wilson estimate: 71.78 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.097 / Net I/σ(I): 4.7 |
Reflection shell | Resolution: 2.6→2.71 Å / Rmerge(I) obs: 1.669 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 2870 / CC1/2: 0.53 / % possible all: 97.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6fxp Resolution: 2.6→46.98 Å / SU ML: 0.4198 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.9573
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 98.66 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→46.98 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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