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- EMDB-11158: Cryo-EM structure of the nitrilase from Pseudomonas fluorescens E... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-11158 | |||||||||
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Title | Cryo-EM structure of the nitrilase from Pseudomonas fluorescens EBC191 at 3.3 Angstroms | |||||||||
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![]() | bacterial nitrilase / arylacetonitrilase / hydrolase | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
![]() | Eppinger E / Stolz A | |||||||||
![]() | ![]() Title: Cryo-EM structure of the nitrilase from Pseudomonas fluorescens EBC191 at 3.3 Angstroms Authors: Eppinger E / Stolz A / Sewell BT | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 9.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.8 KB 10.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.7 KB | Display | ![]() |
Images | ![]() | 107.3 KB | ||
Filedesc metadata | ![]() | 5.3 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 673 KB | Display | ![]() |
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Full document | ![]() | 672.6 KB | Display | |
Data in XML | ![]() | 9.6 KB | Display | |
Data in CIF | ![]() | 13.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6zbyMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.048 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Active helical nitrilase homooligomer
Entire | Name: Active helical nitrilase homooligomer |
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Components |
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-Supramolecule #1: Active helical nitrilase homooligomer
Supramolecule | Name: Active helical nitrilase homooligomer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: NitA
Macromolecule | Name: NitA / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 37.740746 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MTVHKKQYKV AAVQAAPAFL DLEAGVAKAI GLIAQAAAEG ASLVAFPEAW LPGYPWWIWL DSPAGGMRFV QRNFDNALEV GSEPFERLC RAAAQHKIYV VLGFTERSGG TLYLAQAIID DCGRVVATRR KLKPTHVERS VYGEGDGSDL AVHDTTLGRL G ALCCAEHI ...String: MTVHKKQYKV AAVQAAPAFL DLEAGVAKAI GLIAQAAAEG ASLVAFPEAW LPGYPWWIWL DSPAGGMRFV QRNFDNALEV GSEPFERLC RAAAQHKIYV VLGFTERSGG TLYLAQAIID DCGRVVATRR KLKPTHVERS VYGEGDGSDL AVHDTTLGRL G ALCCAEHI QPLSKYAMYA QHEQVHIAAW PSFSVYRGAA FQLSAQANNA ASQVYALEGQ CFVLAPCATV SKEMLDELID SP AKAELLL EGGGFAMIYG PDGAPLCTPL AETEEGILYA DIDLGVIGVA KAAYDPVGHY SRPDVLRLLV NREPMTRVHY VQP QSLPET SVLAFGAGAD AIRSEENPEE QGDK UniProtKB: NitA |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | helical reconstruction |
Aggregation state | filament |
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Sample preparation
Concentration | 0.15 mg/mL |
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Buffer | pH: 7.8 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK I Details: The sample (2.5 ul) was applied to the grid and incubated for 30 seconds at 100% humidity before blotting and plunging.. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number real images: 2929 / Average exposure time: 6.0 sec. / Average electron dose: 43.1 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL / Target criteria: Cross-correlation coefficient |
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Output model | ![]() PDB-6zby: |