+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36749 | |||||||||
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Title | CryoEM structure of the NADP-dependent malic enzyme MaeB | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Type III secretion system / inositol phosphate phosphatase / bacteria effector / LIPID BINDING PROTEIN | |||||||||
Function / homology | Function and homology information malolactic enzyme activity / malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) / malate dehydrogenase (decarboxylating) (NADP+) activity / oxaloacetate decarboxylase activity / malate metabolic process / acyltransferase activity / NAD binding / manganese ion binding / identical protein binding / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (strain K12) (bacteria) / Escherichia coli K-12 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.86 Å | |||||||||
Authors | Jiang WX / Cheng XQ / Wu M / Ma LX / Xing Q | |||||||||
Funding support | China, 1 items
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Citation | Journal: To Be Published Title: CryoEM structure of the NADP-dependent malic enzyme in complex with oxaloacetate Authors: Jiang WX / Cheng XQ / Wu M / Ma LX / Xing Q | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_36749.map.gz | 406.3 MB | EMDB map data format | |
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Header (meta data) | emd-36749-v30.xml emd-36749.xml | 13.2 KB 13.2 KB | Display Display | EMDB header |
Images | emd_36749.png | 95.9 KB | ||
Filedesc metadata | emd-36749.cif.gz | 5.6 KB | ||
Others | emd_36749_half_map_1.map.gz emd_36749_half_map_2.map.gz | 765.5 MB 765.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36749 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36749 | HTTPS FTP |
-Validation report
Summary document | emd_36749_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_36749_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_36749_validation.xml.gz | 20.6 KB | Display | |
Data in CIF | emd_36749_validation.cif.gz | 24.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36749 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36749 | HTTPS FTP |
-Related structure data
Related structure data | 8jzoMC 8k04C 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_36749.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.56667 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_36749_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_36749_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : NADP-dependent malic enzyme
Entire | Name: NADP-dependent malic enzyme |
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Components |
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-Supramolecule #1: NADP-dependent malic enzyme
Supramolecule | Name: NADP-dependent malic enzyme / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Escherichia coli (strain K12) (bacteria) |
-Macromolecule #1: NADP-dependent malic enzyme
Macromolecule | Name: NADP-dependent malic enzyme / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO EC number: malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) |
Molecular weight | Theoretical: 82.507266 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: MDDQLKQSAL DFHEFPVPGK IQVSPTKPLA TQRDLALAYS PGVAAPCLEI EKDPLKAYKY TARGNLVAVI SNGTAVLGLG NIGALAGKP VMEGKGVLFK KFAGIDVFDI EVDELDPDKF IEVVAALEPT FGGINLEDIK APECFYIEQK LRERMNIPVF H DDQHGTAI ...String: MDDQLKQSAL DFHEFPVPGK IQVSPTKPLA TQRDLALAYS PGVAAPCLEI EKDPLKAYKY TARGNLVAVI SNGTAVLGLG NIGALAGKP VMEGKGVLFK KFAGIDVFDI EVDELDPDKF IEVVAALEPT FGGINLEDIK APECFYIEQK LRERMNIPVF H DDQHGTAI ISTAAILNGL RVVEKNISDV RMVVSGAGAA AIACMNLLVA LGLQKHNIVV CDSKGVIYQG REPNMAETKA AY AVVDDGK RTLDDVIEGA DIFLGCSGPK VLTQEMVKKM ARAPMILALA NPEPEILPPL AKEVRPDAII CTGRSDYPNQ VNN VLCFPF IFRGALDVGA TAINEEMKLA AVRAIAELAH AEQSEVVASA YGDQDLSFGP EYIIPKPFDP RLIVKIAPAV AKAA MESGV ATRPIADFDV YIDKLTEFVY KTNLFMKPIF SQARKAPKRV VLPEGEEARV LHATQELVTL GLAKPILIGR PNVIE MRIQ KLGLQIKAGV DFEIVNNESD PRFKEYWTEY FQIMKRRGVT QEQAQRALIS NPTVIGAIMV QRGEADAMIC GTVGDY HEH FSVVKNVFGY RDGVHTAGAM NALLLPSGNT FIADTYVNDE PDAEELAEIT LMAAETVRRF GIEPRVALLS HSNFGSS DC PSSSKMRQAL ELVRERAPEL MIDGEMHGDA ALVEAIRNDR MPDSSLKGSA NILVMPNMEA ARISYNLLRV SSSEGVTV G PVLMGVAKPV HVLTPIASVR RIVNMVALAV VEAQTQPL UniProtKB: NADP-dependent malic enzyme |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.2 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 39.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 108061 |
Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |