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- PDB-4gvs: X-ray structure of the Archaeoglobus fulgidus methenyl-tetrahydro... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4gvs | ||||||
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Title | X-ray structure of the Archaeoglobus fulgidus methenyl-tetrahydromethanopterin cyclohydrolase in complex with N5-formyl-tetrahydromethanopterin | ||||||
![]() | Methenyltetrahydromethanopterin cyclohydrolase | ||||||
![]() | HYDROLASE / N5-formyl-tetrahydromethanopterin | ||||||
Function / homology | ![]() methenyltetrahydromethanopterin cyclohydrolase / methenyltetrahydromethanopterin cyclohydrolase activity / : / one-carbon metabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Upadhyay, V. / Demmer, U. / Warkentin, E. / Moll, J. / Shima, S. / Ermler, U. | ||||||
![]() | ![]() Title: Structure and catalytic mechanism of N(5),N(10)-methenyl-tetrahydromethanopterin cyclohydrolase. Authors: Upadhyay, V. / Demmer, U. / Warkentin, E. / Moll, J. / Shima, S. / Ermler, U. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 206.7 KB | Display | ![]() |
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PDB format | ![]() | 166.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 659.4 KB | Display | ![]() |
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Full document | ![]() | 680.8 KB | Display | |
Data in XML | ![]() | 42.6 KB | Display | |
Data in CIF | ![]() | 61.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4gvqC ![]() 4gvrC ![]() 1qlmS C: citing same article ( 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 domain:
NCS domain segments:
NCS oper:
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Components
#1: Protein | Mass: 34879.637 Da / Num. of mol.: 3 / Mutation: E186Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: O28344, methenyltetrahydromethanopterin cyclohydrolase #2: Chemical | ChemComp-F4M / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.27 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 8% (w/v) PEG 4000, 0.1M ammonium acetate, 0.1M sodium acetate pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
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Detector | Date: Apr 28, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.214 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→43.402 Å / Num. all: 116728 / Num. obs: 108423 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1QLM Resolution: 1.75→43.4 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.204 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 28.853 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→43.4 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 2330 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.75→1.795 Å / Total num. of bins used: 20
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