+Open data
-Basic information
Entry | Database: PDB / ID: 7w8j | ||||||
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Title | Dimethylformamidase, 2x(A2B2) | ||||||
Components |
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Keywords | HYDROLASE / Amidohydrolase / mononuclear iron / AB polypeptide / tetramer | ||||||
Function / homology | N,N-dimethylformamidase / N,N-dimethylformamidase activity / N,N-dimethylformamidase beta subunit-like, C-terminal / N,N-dimethylformamidase beta subunit-like, C-terminal / Concanavalin A-like lectin/glucanases superfamily / Concanavalin A-like lectin/glucanase domain superfamily / : / N,N-dimethylformamidase large subunit / N,N-dimethylformamidase small subunit Function and homology information | ||||||
Biological species | Paracoccus sp. SSG05 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å | ||||||
Authors | Vinothkumar, K.R. / Subramanian, R. / Arya, C. / Ramanathan, G. | ||||||
Funding support | India, 1items
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Citation | Journal: To Be Published Title: Dimethylformamidase with a Unique Iron Center Authors: Arya, C. / Ramanathan, G. / Vinothkumar, K.R. / Subramanian, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7w8j.cif.gz | 631.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7w8j.ent.gz | 527.9 KB | Display | PDB format |
PDBx/mmJSON format | 7w8j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w8/7w8j ftp://data.pdbj.org/pub/pdb/validation_reports/w8/7w8j | HTTPS FTP |
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-Related structure data
Related structure data | 32357MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 86341.758 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paracoccus sp. SSG05 (bacteria) / Gene: dmfase2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I6NT79, N,N-dimethylformamidase #2: Protein | Mass: 16083.823 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paracoccus sp. SSG05 (bacteria) / Gene: dmfase1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I6NWZ0, N,N-dimethylformamidase #3: Chemical | ChemComp-FE / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: DMFase, an amidohydrolase / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT | |||||||||||||||
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Molecular weight | Value: 0.4 MDa / Experimental value: YES | |||||||||||||||
Source (natural) | Organism: Paracoccus sp. (bacteria) / Strain: SSG05 | |||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) / Strain: BL21 (DE3) | |||||||||||||||
Buffer solution | pH: 7.2 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Enzyme after gel filtration was used for cryoEM grid prep. Sample was held at 37 degrees before application on the grid. | |||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 291 K / Details: wait time - 10 seconds and 3.5 seconds blot |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 75000 X / Calibrated magnification: 130841 X / Nominal defocus max: 3200 nm / Nominal defocus min: 850 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (min): 79 K |
Image recording | Average exposure time: 60 sec. / Electron dose: 28.3 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 548 Details: One image was collected per hole. Total of 25 frames was saved and each frame has ~1.13 e/A2 |
Image scans | Sampling size: 14 µm / Width: 4096 / Height: 4096 |
-Processing
Software | Name: REFMAC / Version: 5.8.0267 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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Image processing | Details: From the 548 images, MotionCor2 was used for full frame alignment. After CTF estimation, 528 micrographs were selected and used for further extraction. Two rounds of 2D classification of ...Details: From the 548 images, MotionCor2 was used for full frame alignment. After CTF estimation, 528 micrographs were selected and used for further extraction. Two rounds of 2D classification of extracted particles resulted in 30689 particles and used for refinement. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 114182 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 28964 / Algorithm: BACK PROJECTION Details: The final reconstruction was from a single 3D class after B-factor weighting and aberration correction in Relion 3.1 Num. of class averages: 1 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 73.98 / Protocol: OTHER / Space: RECIPROCAL Details: Servalcat was used along with Refmac to calculate fofc maps and extensively used for modelling. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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Refinement | Resolution: 2.5→160.5 Å / Cor.coef. Fo:Fc: 0.933 / SU B: 9.317 / SU ML: 0.197 / ESU R: 0.287 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Solvent model: PARAMETERS FOR MASK CACLULATION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 73.986 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Total: 28678 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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