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- PDB-4fio: Crystal Structure of Methenyltetrahydromethanopterin Cyclohydrola... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4fio | ||||||
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Title | Crystal Structure of Methenyltetrahydromethanopterin Cyclohydrolase from Methanobrevibacter ruminantium | ||||||
![]() | Methenyltetrahydromethanopterin cyclohydrolase | ||||||
![]() | HYDROLASE / methanogenesis / hydrolysis | ||||||
Function / homology | ![]() methenyltetrahydromethanopterin cyclohydrolase / methenyltetrahydromethanopterin cyclohydrolase activity / methanogenesis, from carbon dioxide / one-carbon metabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Carbone, V. / Schofield, L.R. / Beattie, A.K. / Sutherland-Smith, A.J. / Ronimus, R.S. | ||||||
![]() | ![]() Title: The crystal structure of methenyltetrahydromethanopterin cyclohydrolase from Methanobrevibacter ruminantium. Authors: Carbone, V. / Schofield, L.R. / Beattie, A.K. / Sutherland-Smith, A.J. / Ronimus, R.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 417.8 KB | Display | ![]() |
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PDB format | ![]() | 340.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 482 KB | Display | ![]() |
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Full document | ![]() | 497.7 KB | Display | |
Data in XML | ![]() | 48 KB | Display | |
Data in CIF | ![]() | 73.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1qlmS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 37741.852 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 35063 / DSM 1093 / JCM 13430 / M1 / Gene: mch, mru_1619 / Plasmid: pET151D / Production host: ![]() ![]() References: UniProt: D3E4S5, methenyltetrahydromethanopterin cyclohydrolase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8.5 Details: 0.2 M sodium acetate, 0.1 M Tris-HCl, 30% (w/v) PEG 4000 and 3% (v/v) isopropanol, pH 8.5, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 28, 2011 |
Radiation | Monochromator: SI VORTEX-ES / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953691 Å / Relative weight: 1 |
Reflection | Resolution: 1.37→19.88 Å / Num. obs: 184543 / % possible obs: 93.8 % / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 1.37→1.44 Å / Rmerge(I) obs: 0.606 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.606 / % possible all: 79.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1QLM Resolution: 1.37→19.88 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.612 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.011 / ESU R Free: 0.012 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 18.55 Å2
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Refine analyze | Luzzati coordinate error obs: 0.144 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.37→19.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.37→1.4 Å / Total num. of bins used: 20
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