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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-12938 | |||||||||
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Title | Cryo-EM structure of Medicago truncatula HISN5 protein | |||||||||
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![]() | histidine biosynthesis / herbicide design / high-resolution Cryo-EM / LYASE | |||||||||
Function / homology | ![]() imidazoleglycerol-phosphate dehydratase / imidazoleglycerol-phosphate dehydratase activity / L-histidine biosynthetic process Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.4 Å | |||||||||
![]() | Ruszkowski M / Witek W | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM and crystal structures of a herbicide development target, HISN5 Authors: Witek W / Ruszkowski M | |||||||||
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 | ![]() | 155.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 11.2 KB 11.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 12.4 KB | Display | ![]() |
Images | ![]() | 376.4 KB | ||
Filedesc metadata | ![]() | 5.4 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 445.8 KB | Display | ![]() |
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Full document | ![]() | 445.4 KB | Display | |
Data in XML | ![]() | 12.5 KB | Display | |
Data in CIF | ![]() | 17 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7oj5MC 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: 0.86 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 : Medicago truncatula HISN5 protein
Entire | Name: Medicago truncatula HISN5 protein |
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Components |
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-Supramolecule #1: Medicago truncatula HISN5 protein
Supramolecule | Name: Medicago truncatula HISN5 protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: Imidazoleglycerol-phosphate dehydratase |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Imidazoleglycerol-phosphate dehydratase
Macromolecule | Name: Imidazoleglycerol-phosphate dehydratase / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO / EC number: imidazoleglycerol-phosphate dehydratase |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 22.692453 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MSTFPIDSGA RIGEMKRVTK ETNVSVKINL DGTGVADNSS GIPFLDHMLD QLASHGLFDV HVKATGDTHI DDHHTNEDVA LAIGTALLQ ALGDRKGINR FGNFSAPLDE ALVHVSLDLS GRPHLGYDLN IPTQRVGKYD TQLVEHFFQS LVNTSGMTLH I RQFSGTNS ...String: MSTFPIDSGA RIGEMKRVTK ETNVSVKINL DGTGVADNSS GIPFLDHMLD QLASHGLFDV HVKATGDTHI DDHHTNEDVA LAIGTALLQ ALGDRKGINR FGNFSAPLDE ALVHVSLDLS GRPHLGYDLN IPTQRVGKYD TQLVEHFFQS LVNTSGMTLH I RQFSGTNS HHIIEATFKA FARALRQATE YDTRRRGTIP SSKGVLSRS UniProtKB: Imidazoleglycerol-phosphate dehydratase |
-Macromolecule #2: MANGANESE (II) ION
Macromolecule | Name: MANGANESE (II) ION / type: ligand / ID: 2 / Number of copies: 48 / Formula: MN |
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Molecular weight | Theoretical: 54.938 Da |
-Macromolecule #3: water
Macromolecule | Name: water / type: ligand / ID: 3 / Number of copies: 931 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ![]() ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Number grids imaged: 1 / Number real images: 1008 / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |