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Yorodumi- PDB-1m5s: Formylmethanofuran:tetrahydromethanopterin fromyltransferase from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1m5s | ||||||
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Title | Formylmethanofuran:tetrahydromethanopterin fromyltransferase from Methanosarcina barkeri | ||||||
Components | Formylmethanofuran--tetrahydromethanopterin formyltransferase | ||||||
Keywords | TRANSFERASE / ALPHA/BETA SANDWICH | ||||||
Function / homology | Function and homology information formylmethanofuran-tetrahydromethanopterin N-formyltransferase / formylmethanofuran-tetrahydromethanopterin N-formyltransferase activity / methanogenesis, from carbon dioxide / one-carbon metabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | Methanosarcina barkeri (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Mamat, B. / Roth, A. / Grimm, C. / Ermler, U. / Tziatzios, C. / Schubert, D. / Thauer, R.K. / Shima, S. | ||||||
Citation | Journal: Protein Sci. / Year: 2002 Title: Crystal structures and enzymatic properties of three formyltransferases from archaea: environmental adaptation and evolutionary relationship. Authors: Mamat, B. / Roth, A. / Grimm, C. / Ermler, U. / Tziatzios, C. / Schubert, D. / Thauer, R.K. / Shima, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1m5s.cif.gz | 245.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m5s.ent.gz | 195.8 KB | Display | PDB format |
PDBx/mmJSON format | 1m5s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1m5s_validation.pdf.gz | 448.6 KB | Display | wwPDB validaton report |
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Full document | 1m5s_full_validation.pdf.gz | 464.9 KB | Display | |
Data in XML | 1m5s_validation.xml.gz | 50.8 KB | Display | |
Data in CIF | 1m5s_validation.cif.gz | 71.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m5/1m5s ftp://data.pdbj.org/pub/pdb/validation_reports/m5/1m5s | HTTPS FTP |
-Related 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: 31695.168 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanosarcina barkeri (archaea) / Plasmid: pET24b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P55301, formylmethanofuran-tetrahydromethanopterin N-formyltransferase #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: 2.52 Å3/Da / Density % sol: 51.15 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: MPD, sodium citrate, ammonium acetate, HEPES, formylmethanofuran, pH 6.7, VAPOR DIFFUSION, HANGING DROP at 277K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7 | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.85→30 Å / Num. all: 106340 / Num. obs: 99960 / % possible obs: 94 % / Observed criterion σ(I): 1 / Biso Wilson estimate: 19.3 Å2 / Rsym value: 0.037 |
Reflection shell | Resolution: 1.85→1.92 Å / Rsym value: 0.081 / % possible all: 84.4 |
Reflection | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 30 Å / % possible obs: 94 % / Num. measured all: 215926 / Rmerge(I) obs: 0.037 |
Reflection shell | *PLUS Highest resolution: 1.88 Å / % possible obs: 84.4 % / Rmerge(I) obs: 0.081 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Formylmethanofuran:tetrahydromethanopterin formyltransferase from Methanopyrus kandleri Resolution: 1.85→19.78 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 58.317 Å2 / ksol: 0.339322 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.9 Å2
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Refine analyze | Luzzati coordinate error free: 0.29 Å / Luzzati sigma a free: 0.26 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→19.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.97 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Rfactor all: 0.197 / Rfactor Rfree: 0.248 / Rfactor Rwork: 0.197 / Highest resolution: 1.9 Å / Lowest resolution: 30 Å | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.325 / Rfactor Rwork: 0.285 |