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- PDB-3wvc: Guanylylpyridinol (GP)-bound HcgF from Methanocaldococcus jannaschii -
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Open data
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Basic information
Entry | Database: PDB / ID: 3wvc | ||||||
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Title | Guanylylpyridinol (GP)-bound HcgF from Methanocaldococcus jannaschii | ||||||
![]() | UPF0254 protein MJ1251 | ||||||
![]() | HYDROLASE / Thioesterase | ||||||
Function / homology | FeGP cofactor biosynthesis protein HcgF / FeGP cofactor biosynthesis protein HcgF / Chem-FEG / Chem-ZGP / UPF0254 protein MJ1251![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fujishiro, T. / Ermler, U. / Shima, S. | ||||||
![]() | ![]() Title: Protein-pyridinol thioester precursor for biosynthesis of the organometallic acyl-iron ligand in [Fe]-hydrogenase cofactor Authors: Fujishiro, T. / Kahnt, J. / Ermler, U. / Shima, 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 | ![]() | 153 KB | Display | ![]() |
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PDB format | ![]() | 119.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 18.7 KB | Display | |
Data in CIF | ![]() | 26.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3wv7C ![]() 3wv8C ![]() 3wv9C ![]() 3wvaSC ![]() 3wvbC 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: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: _ / Auth seq-ID: -1 - 167 / Label seq-ID: 2 - 170
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Components
#1: Protein | Mass: 19254.324 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440 Gene: MJ1251 / Plasmid: pET28b / Production host: ![]() ![]() References: UniProt: Q58649, Hydrolases; Acting on ester bonds; Thioester hydrolases #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-ZGP / | #4: Chemical | ChemComp-FEG / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.14 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 40%(v/v)MPD, 200mM lithium sulfate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 30, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: A Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→50 Å / Num. obs: 22368 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 20.35 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: SeMet-labelled HcgF from Methanocaldococcus jannaschii PDB ENTRY 3WVA Resolution: 2→48.76 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.913 / SU B: 8.13 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.193 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
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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: 22.807 Å2
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Refinement step | Cycle: LAST / Resolution: 2→48.76 Å
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Refine LS restraints |
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