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Yorodumi- PDB-4gvr: X-ray structure of the Archaeoglobus fulgidus methenyl-tetrahydro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4gvr | ||||||
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Title | X-ray structure of the Archaeoglobus fulgidus methenyl-tetrahydromethanopterin cyclohydrolase | ||||||
Components | Methenyltetrahydromethanopterin cyclohydrolase | ||||||
Keywords | HYDROLASE / methenyl-tetrahydromethanopterin / N5-formyl-tetrahydromethanopterin | ||||||
Function / homology | Function and homology information methenyltetrahydromethanopterin cyclohydrolase / methenyltetrahydromethanopterin cyclohydrolase activity / : / one-carbon metabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | Archaeoglobus fulgidus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å | ||||||
Authors | Upadhyay, V. / Demmer, U. / Warkentin, E. / Moll, J. / Shima, S. / Ermler, U. | ||||||
Citation | Journal: Biochemistry / Year: 2012 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gvr.cif.gz | 410.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gvr.ent.gz | 339 KB | Display | PDB format |
PDBx/mmJSON format | 4gvr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4gvr_validation.pdf.gz | 443 KB | Display | wwPDB validaton report |
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Full document | 4gvr_full_validation.pdf.gz | 457.4 KB | Display | |
Data in XML | 4gvr_validation.xml.gz | 43.1 KB | Display | |
Data in CIF | 4gvr_validation.cif.gz | 64 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gv/4gvr ftp://data.pdbj.org/pub/pdb/validation_reports/gv/4gvr | HTTPS FTP |
-Related structure data
Related structure data | 4gvqC 4gvsC 1qlmS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-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.) Archaeoglobus fulgidus (archaea) / Strain: DSM 4304 / Gene: AF_1935, mch / Plasmid: pET-24a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS References: UniProt: O28344, methenyltetrahydromethanopterin cyclohydrolase #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: 2.71 Å3/Da / Density % sol: 54.63 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 10% (w/v) PEG 4000, 10% (v/v) Isopropanol, 0.1M Sodium acetate pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.0001 Å |
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Detector | Date: Dec 8, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0001 Å / Relative weight: 1 |
Reflection | Resolution: 1.52→48.17 Å / Num. all: 170753 / Num. obs: 164493 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1QLM Resolution: 1.52→48.17 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.941 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.083 / 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: 25.003 Å2
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Refinement step | Cycle: LAST / Resolution: 1.52→48.17 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 2347 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.52→1.559 Å / Total num. of bins used: 20
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