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Yorodumi- PDB-8tms: Crystal structure of bacterial pectin methylesterase PmeC2 from r... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8tms | ||||||
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Title | Crystal structure of bacterial pectin methylesterase PmeC2 from rumen Butyrivibrio | ||||||
Components | Pectinesterase | ||||||
Keywords | SUGAR BINDING PROTEIN / Pectin methylesterase / Butyrivibrio / rumen / pectin / methanol / methane | ||||||
Function / homology | Function and homology information pectinesterase / pectinesterase activity / : / cell wall modification / pectin catabolic process Similarity search - Function | ||||||
Biological species | Butyrivibrio fibrisolvens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Carbone, V. / Reilly, K. / Sang, C. / Schofield, L. / Ronimus, R. / Kelly, W.J. / Attwood, G.T. / Palevich, N. | ||||||
Funding support | New Zealand, 1items
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Citation | Journal: Int J Mol Sci / Year: 2023 Title: Crystal Structures of Bacterial Pectin Methylesterases Pme8A and PmeC2 from Rumen Butyrivibrio . Authors: Carbone, V. / Reilly, K. / Sang, C. / Schofield, L.R. / Ronimus, R.S. / Kelly, W.J. / Attwood, G.T. / Palevich, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8tms.cif.gz | 475.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8tms.ent.gz | 391.2 KB | Display | PDB format |
PDBx/mmJSON format | 8tms.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8tms_validation.pdf.gz | 478.9 KB | Display | wwPDB validaton report |
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Full document | 8tms_full_validation.pdf.gz | 489 KB | Display | |
Data in XML | 8tms_validation.xml.gz | 44.2 KB | Display | |
Data in CIF | 8tms_validation.cif.gz | 60.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tm/8tms ftp://data.pdbj.org/pub/pdb/validation_reports/tm/8tms | HTTPS FTP |
-Related structure data
Related structure data | 8tneC 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 34418.730 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Butyrivibrio fibrisolvens (bacteria) / Gene: SAMN02745229_01989 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1M5Z711 #2: Chemical | #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.57 Å3/Da / Density % sol: 51.7 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M Tris pH 8.5, 20 % w/v PEG 8000 |
-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: 0.95372 Å |
Detector | Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Mar 31, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→47.2 Å / Num. obs: 56000 / % possible obs: 95.1 % / Redundancy: 3.7 % / CC1/2: 0.994 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.089 / Rrim(I) all: 0.173 / Χ2: 0.49 / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 2.3→2.37 Å / % possible obs: 92.3 % / Redundancy: 3.6 % / Rmerge(I) obs: 1.404 / Num. measured all: 16208 / Num. unique obs: 4465 / CC1/2: 0.349 / Rpim(I) all: 0.842 / Rrim(I) all: 1.639 / Χ2: 0.47 / Net I/σ(I) obs: 0.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→47.17 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.928 / SU B: 24.799 / SU ML: 0.26 / Cross valid method: THROUGHOUT / ESU R: 0.391 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.514 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→47.17 Å
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