+Open data
-Basic information
Entry | Database: PDB / ID: 8jzo | ||||||
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Title | CryoEM structure of the NADP-dependent malic enzyme MaeB | ||||||
Components | NADP-dependent malic enzyme | ||||||
Keywords | LIPID BINDING PROTEIN / Type III secretion system / inositol phosphate phosphatase / bacteria effector | ||||||
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 K-12 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.86 Å | ||||||
Authors | Jiang, W.X. / Cheng, X.Q. / Wu, M. / Ma, L.X. / Xing, Q. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: CryoEM structure of the NADP-dependent malic enzyme in complex with oxaloacetate Authors: Jiang, W.X. / Cheng, X.Q. / Wu, M. / Ma, L.X. / Xing, Q. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8jzo.cif.gz | 746 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8jzo.ent.gz | 616.1 KB | Display | PDB format |
PDBx/mmJSON format | 8jzo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8jzo_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8jzo_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8jzo_validation.xml.gz | 122.2 KB | Display | |
Data in CIF | 8jzo_validation.cif.gz | 185.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jz/8jzo ftp://data.pdbj.org/pub/pdb/validation_reports/jz/8jzo | HTTPS FTP |
-Related structure data
Related structure data | 36749MC 8k04C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 1 - 759 / Label seq-ID: 1 - 759
NCS oper:
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-Components
#1: Protein | Mass: 82507.266 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: maeB, ypfF, b2463, JW2447 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P76558, malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: NADP-dependent malic enzyme / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Escherichia coli (strain K12) (bacteria) |
Source (recombinant) | Organism: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others) |
Buffer solution | pH: 7.2 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: DIFFRACTION / Nominal defocus max: 1500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 39 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||
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3D reconstruction | Resolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 108061 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 155.02 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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Refine LS restraints NCS |
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