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Yorodumi- EMDB-19910: Cyanide dihydratase from Bacillus pumilus C1 E155R variant with a... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19910 | |||||||||
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Title | Cyanide dihydratase from Bacillus pumilus C1 E155R variant with altered helical twist. | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Left-handed helix. / HYDROLASE | |||||||||
Function / homology | Nitrilase/Cyanide hydratase / Nitrilases / cyanide hydratase signature 1. / Nitrilase/cyanide hydratase, conserved site / nitrilase activity / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase / Cyanide dihydratase Function and homology information | |||||||||
Biological species | Bacillus pumilus (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
Authors | Dlamini LS / Woodward JD / Sewell BT | |||||||||
Funding support | South Africa, 1 items
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Citation | Journal: To Be Published Title: Cyanide dihydratase from Bacillus pumilus C1 E155R variant with altered helical twist Authors: Dlamini LS / Woodward JD / Sewell BT | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_19910.map.gz | 166.6 MB | EMDB map data format | |
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Header (meta data) | emd-19910-v30.xml emd-19910.xml | 16.2 KB 16.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_19910_fsc.xml | 12.8 KB | Display | FSC data file |
Images | emd_19910.png | 48.4 KB | ||
Filedesc metadata | emd-19910.cif.gz | 6 KB | ||
Others | emd_19910_half_map_1.map.gz emd_19910_half_map_2.map.gz | 139.6 MB 139.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19910 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19910 | HTTPS FTP |
-Validation report
Summary document | emd_19910_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_19910_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_19910_validation.xml.gz | 20.1 KB | Display | |
Data in CIF | emd_19910_validation.cif.gz | 26.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19910 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19910 | HTTPS FTP |
-Related structure data
Related structure data | 9er3MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_19910.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.825 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_19910_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_19910_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cyanide dihydratase from Bacillus pumilus C1 E155R variant with a...
Entire | Name: Cyanide dihydratase from Bacillus pumilus C1 E155R variant with altered helical twist. |
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Components |
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-Supramolecule #1: Cyanide dihydratase from Bacillus pumilus C1 E155R variant with a...
Supramolecule | Name: Cyanide dihydratase from Bacillus pumilus C1 E155R variant with altered helical twist. type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Bacillus pumilus (bacteria) |
Molecular weight | Theoretical: 703 KDa |
-Macromolecule #1: Cyanide dihydratase
Macromolecule | Name: Cyanide dihydratase / type: protein_or_peptide / ID: 1 / Number of copies: 19 / Enantiomer: LEVO |
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Source (natural) | Organism: Bacillus pumilus (bacteria) |
Molecular weight | Theoretical: 36.19873 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: TSIYPKFRAA AVQAAPIYLN LEASVEKSCE LIDEAASNGA KLVAFPEAFL PGYPWFAFIG HPEYTRKFYH ELYKNAVEIP SLAIQKISE AAKRNETYVC ISCSEKDGGS LYLAQLWFNP NGDLIGKHRK MRASVAERLI WGDGSGSMMP VFQTRIGNLG G LMCWEHQV ...String: TSIYPKFRAA AVQAAPIYLN LEASVEKSCE LIDEAASNGA KLVAFPEAFL PGYPWFAFIG HPEYTRKFYH ELYKNAVEIP SLAIQKISE AAKRNETYVC ISCSEKDGGS LYLAQLWFNP NGDLIGKHRK MRASVAERLI WGDGSGSMMP VFQTRIGNLG G LMCWEHQV PLDLMAMNAQ NEQVHVASWP GYFDDEISSR YYAIATQTFV LMTSSIYTEE MKEMICLTQE QRDYFETFKS GH TCIYGPD GEPISDMVPA ETEGIAYAEI DVERVIDYKY YIDPAGHYSN QSLSMNFNQQ PTPVVKHLNH QKNEVFTYED IQ UniProtKB: Cyanide dihydratase |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 1.8 mg/mL |
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Buffer | pH: 7.4 / Component - Concentration: 50.0 mM / Component - Formula: Tris-HCl / Component - Name: Tris-(hydroxymethyl) aminomethane / Details: 50 mM NaCL, 50 mM Tris-HCl |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 2.0 kPa |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK I |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 31418 / Average exposure time: 2.04 sec. / Average electron dose: 1.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | Chain - Source name: Other / Chain - Initial model type: other Details: The initial model was built ab initio using the map and amino acid sequence. |
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Refinement | Space: REAL / Protocol: AB INITIO MODEL / Overall B value: 101.248 / Target criteria: Cross-correlation coefficient |
Output model | PDB-9er3: |