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Yorodumi- PDB-7tzi: Structure of a pseudomurein peptide ligase type E from Methanothe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7tzi | ||||||
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Title | Structure of a pseudomurein peptide ligase type E from Methanothermobacter thermautotrophicus | ||||||
Components | Mur ligase family protein | ||||||
Keywords | LIGASE / Pseudomurein / pseudomurein peptide ligase / archaeal cell wall / Methanothermobacter thermautotrophicus / pMurE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Methanothermobacter thermautotrophicus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.911 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 | 7tzi.cif.gz | 177.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7tzi.ent.gz | 140.4 KB | Display | PDB format |
PDBx/mmJSON format | 7tzi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7tzi_validation.pdf.gz | 433.5 KB | Display | wwPDB validaton report |
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Full document | 7tzi_full_validation.pdf.gz | 441.6 KB | Display | |
Data in XML | 7tzi_validation.xml.gz | 31.1 KB | Display | |
Data in CIF | 7tzi_validation.cif.gz | 42.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tz/7tzi ftp://data.pdbj.org/pub/pdb/validation_reports/tz/7tzi | HTTPS FTP |
-Related structure data
Related structure data | 6vr8C 7jt8SC 7ufpC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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: 48967.402 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea) Gene: HA285_03230 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7J4MVA9 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 100 mM amino acids mix; 0.1 M buffer system 6, pH 8.5; 50% v/v precipitant mix of 25% w/v PEG4000 and 40% w/v 1,2,6-hexanetriol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.987 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 23, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.91→47.24 Å / Num. obs: 25647 / % possible obs: 99.5 % / Redundancy: 13.6 % / Biso Wilson estimate: 68.4 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.1 / Net I/σ(I): 3.92 |
Reflection shell | Resolution: 2.91→2.94 Å / Num. unique obs: 3964 / CC1/2: 0.834 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7JT8 Resolution: 2.911→46.29 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.919 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.365
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Displacement parameters | Biso mean: 74.98 Å2
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Refine analyze | Luzzati coordinate error obs: 0.39 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.911→46.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.911→2.94 Å
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