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- PDB-9kru: B. bacteriovorus MaeB holo form -

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Basic information

Entry
Database: PDB / ID: 9kru
TitleB. bacteriovorus MaeB holo form
ComponentsNADP-dependent malic enzyme
KeywordsSTRUCTURAL PROTEIN / oxidoreductase / cryo-EM / allostery
Function / homology
Function and homology information


malic enzyme activity / malate metabolic process / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / acyltransferase activity / NAD binding / metal ion binding
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, N-terminal domain / Malic enzyme, N-terminal domain / Malic enzyme, NAD-binding ...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, 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 NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NADP-dependent malic enzyme
Similarity search - Component
Biological speciesBdellovibrio bacteriovorus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.59 Å
AuthorsSassa, M. / Yamato, H. / Tanino, H. / Fukuda, Y. / Inoue, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: To Be Published
Title: Malic enzymes from different bacteria evolved distinct effector binding sites showing the same allosteric regulation mechanism
Authors: Sassa, M. / Yamato, H. / Tanino, H. / Fukuda, Y. / Inoue, T.
History
DepositionNov 28, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 1.0Dec 3, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
A: NADP-dependent malic enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,1092
Polymers84,3661
Non-polymers7431
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein NADP-dependent malic enzyme


Mass: 84365.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bdellovibrio bacteriovorus (bacteria) / Gene: B9G79_09885 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1Z3N8R4
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Malic enzyme B from Bdellovibrio bacteriovorus strain SSB218315 holo form
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Bdellovibrio bacteriovorus (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
11.0 mMsodium magnesiumMgCl21
23.0 mMNicotinamide adenine dinucleotide phosphateNADP+1
320 mMHEPES1
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 20 mA current / Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K
Details: 3 microliters droplet, 3 seconds delay before blotting, 3 seconds blot, 0 second delay before plunging.

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 200
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 700 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9099

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2SerialEMimage acquisition
4cryoSPARCCTF correction
7UCSF Chimeramodel fitting
9PHENIXmodel refinement
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: D3 (2x3 fold dihedral)
3D reconstructionResolution: 2.59 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 449060 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 45.83 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00235966
ELECTRON MICROSCOPYf_angle_d0.52288088
ELECTRON MICROSCOPYf_chiral_restr0.042921
ELECTRON MICROSCOPYf_plane_restr0.00371054
ELECTRON MICROSCOPYf_dihedral_angle_d6.1972890

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