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Yorodumi- PDB-1y60: Structure of the tetrahydromethanopterin dependent formaldehyde-a... -
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-Basic information
Entry | Database: PDB / ID: 1y60 | ||||||
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Title | Structure of the tetrahydromethanopterin dependent formaldehyde-activating enzyme (Fae) from Methylobacterium extorquens AM1 with bound 5,10-methylene tetrahydromethanopterin | ||||||
Components | Formaldehyde-activating enzyme fae | ||||||
Keywords | LYASE / Pentamer / beta-alpha-beta left handed crossover / TETRAHYDROMETHANOPTERIN-BINDING | ||||||
Function / homology | Function and homology information 5,6,7,8-tetrahydromethanopterin hydro-lyase / carbon-nitrogen lyase activity / formaldehyde catabolic process / carbohydrate biosynthetic process / one-carbon metabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | Methylobacterium extorquens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Acharya, P. / Goenrich, M. / Hagemeier, C.H. / Demmer, U. / Vorholt, J.A. / Thauer, R.K. / Ermler, U. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: How an enzyme binds the C1-carrier tetrahydromethanopterin: Structure of the tetrahydromethanopterin dependent formaldehyde-activating enzyme (Fae) from Methylobacterium extorquens AM1 Authors: Acharya, P. / Goenrich, M. / Hagemeier, C.H. / Demmer, U. / Vorholt, J.A. / Thauer, R.K. / Ermler, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1y60.cif.gz | 186.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1y60.ent.gz | 146.6 KB | Display | PDB format |
PDBx/mmJSON format | 1y60.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1y60_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 1y60_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 1y60_validation.xml.gz | 43.2 KB | Display | |
Data in CIF | 1y60_validation.cif.gz | 57.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y6/1y60 ftp://data.pdbj.org/pub/pdb/validation_reports/y6/1y60 | HTTPS FTP |
-Related structure data
Related structure data | 1y5ySC 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: 17978.391 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Details: complexed with pterin-related cofactor / Source: (gene. exp.) Methylobacterium extorquens (bacteria) / Strain: AM1 / Gene: fae / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9FA38 #2: Chemical | ChemComp-H4M / #3: 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 Å3/Da / Density % sol: 38 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M HEPES/NaOH pH 7.5, 20% (w/v) polyethyleneglycol 10,000, 5 mM tetrahydromethanopterin (H4MPT), VAPOR DIFFUSION, HANGING DROP, temperature 281.0K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93927 Å |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Dec 7, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93927 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→44.82 Å / Num. all: 59516 / Num. obs: 57191 / % possible obs: 93.5 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.144 / Rsym value: 0.082 / Net I/σ(I): 12.15 |
Reflection shell | Resolution: 1.9→2.01 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.03 / Num. unique all: 8288 / Rsym value: 0.4 / % possible all: 76.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Formaldehyde-activating enzyme from Methylobacterium extorquens AM1 PDB ID 1Y5Y Resolution: 1.9→44.82 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 108436.21 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 53.4963 Å2 / ksol: 0.390567 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→44.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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