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- EMDB-36749: CryoEM structure of the NADP-dependent malic enzyme MaeB -

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Basic information

Entry
Database: EMDB / ID: EMD-36749
TitleCryoEM structure of the NADP-dependent malic enzyme MaeB
Map data
Sample
  • Complex: NADP-dependent malic enzyme
    • Protein or peptide: NADP-dependent malic enzyme
KeywordsType 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
NAD(P)-dependent malic enzyme / Malic enzyme, NAD-binding domain, bacterial type / : / Phosphate acetyltransferase, domain 2 / Phosphate acetyltransferase, domain 1 / Phosphate acetyl/butaryl transferase / Phosphate acetyl/butaryl transferase / Malic enzyme, conserved site / Malic enzymes signature. / Malic enzyme, N-terminal domain ...NAD(P)-dependent malic enzyme / Malic enzyme, NAD-binding domain, bacterial type / : / Phosphate acetyltransferase, domain 2 / Phosphate acetyltransferase, domain 1 / Phosphate acetyl/butaryl transferase / Phosphate acetyl/butaryl transferase / Malic enzyme, conserved site / Malic enzymes signature. / Malic enzyme, N-terminal domain / Malic enzyme, N-terminal domain / Malic enzyme, NAD-binding / Malic enzyme, N-terminal domain superfamily / Malic enzyme, N-terminal domain / Malic enzyme, NAD binding domain / Malic enzyme, NAD binding domain / Aminoacid dehydrogenase-like, N-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NADP-dependent malic enzyme
Similarity search - Component
Biological speciesEscherichia coli (strain K12) (bacteria) / Escherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.86 Å
AuthorsJiang WX / Cheng XQ / Wu M / Ma LX / Xing Q
Funding support China, 1 items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program)2021YFC2100100 China
CitationJournal: 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
DepositionJul 6, 2023-
Header (metadata) releaseJul 10, 2024-
Map releaseJul 10, 2024-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_36749.png

Downloads & links

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Map

FileDownload / File: emd_36749.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.57 Å/pix.
x 600 pix.
= 340.002 Å		0.57 Å/pix.
x 600 pix.
= 340.002 Å		0.57 Å/pix.
x 600 pix.
= 340.002 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.56667 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0278
Minimum - Maximum-0.08698845 - 0.21035638
Average (Standard dev.)-0.00008268104 (±0.0066668605)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 340.002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_36749_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_36749_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : NADP-dependent malic enzyme

EntireName: NADP-dependent malic enzyme
Components
  • Complex: NADP-dependent malic enzyme
    • Protein or peptide: NADP-dependent malic enzyme

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Supramolecule #1: NADP-dependent malic enzyme

SupramoleculeName: NADP-dependent malic enzyme / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)

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Macromolecule #1: NADP-dependent malic enzyme

MacromoleculeName: NADP-dependent malic enzyme / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
EC number: malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+)
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 82.507266 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 39.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 108061
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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