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Yorodumi- PDB-7jt8: Apo structure of a pseudomurein peptide ligase type E from Methan... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7jt8 | ||||||
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Title | Apo structure of a pseudomurein peptide ligase type E from Methanothermus fervidus | ||||||
Components | Mur ligase middle domain protein | ||||||
Keywords | LIGASE / Pseudomurein / pseudomurein peptide ligase / archaeal cell wall / Methanothermus fervidus / pMurE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Methanothermus fervidus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å | ||||||
Authors | Carbone, V. / Schofield, L.R. / Sutherland-Smith, A.J. / Ronimus, R.S. / Subedi, B.P. | ||||||
Funding support | New Zealand, 1items
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Citation | Journal: Microbiology (Reading, Engl.) / Year: 2022 Title: Structural characterisation of methanogen pseudomurein cell wall peptide ligases homologous to bacterial MurE/F murein peptide ligases. Authors: Subedi, B.P. / Schofield, L.R. / Carbone, V. / Wolf, M. / Martin, W.F. / Ronimus, R.S. / Sutherland-Smith, A.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7jt8.cif.gz | 146.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jt8.ent.gz | 90.7 KB | Display | PDB format |
PDBx/mmJSON format | 7jt8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jt/7jt8 ftp://data.pdbj.org/pub/pdb/validation_reports/jt/7jt8 | HTTPS FTP |
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-Related structure data
Related structure data | 6vr8C 7tziC 7ufpC 4qdiS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 54251.297 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanothermus fervidus (strain ATCC 43054 / DSM 2088 / JCM 10308 / V24 S) (archaea) Strain: ATCC 43054 / DSM 2088 / JCM 10308 / V24 S / Gene: Mfer_0762 / Plasmid: pET15b / Production host: Escherichia coli BL21 (bacteria) References: UniProt: E3GZ29, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase | ||||
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#2: Chemical | ChemComp-MG / | ||||
#3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.4 / Details: 0.2 M ammonium sulfate, 30% w/v PEG4000, pH 5.4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 18, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→34.58 Å / Num. obs: 50277 / % possible obs: 99.85 % / Redundancy: 22.4 % / Biso Wilson estimate: 21.37 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.091 / Net I/σ(I): 29.3 |
Reflection shell | Resolution: 1.84→1.87 Å / Rmerge(I) obs: 0.878 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 3066 / CC1/2: 0.91 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4QDI Resolution: 1.84→34.58 Å / SU ML: 0.1876 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.5106 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.03 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.84→34.58 Å
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Refine LS restraints |
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LS refinement shell |
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