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Yorodumi- PDB-8k0a: CryoEM structure of 3-phenylpropionate/cinnamic acid dioxygenase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8k0a | ||||||
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Title | CryoEM structure of 3-phenylpropionate/cinnamic acid dioxygenase HcaE-HcaF complex | ||||||
Components |
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Keywords | BIOSYNTHETIC PROTEIN / 3-phenylpropionate/cinnamic acid dioxygenase | ||||||
Function / homology | Function and homology information 3-phenylpropanoate dioxygenase / 3-phenylpropionate dioxygenase activity / 3-phenylpropionate dioxygenase complex / 3-phenylpropionate catabolic process / 2 iron, 2 sulfur cluster binding / iron ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.12 Å | ||||||
Authors | Jiang, W.X. / Cheng, X.Q. / Ma, L.X. / Xing, Q. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: CryoEM structure of 3-phenylpropionate/cinnamic acid dioxygenase HcaE-HcaF complex 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 | 8k0a.cif.gz | 332.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8k0a.ent.gz | 267.4 KB | Display | PDB format |
PDBx/mmJSON format | 8k0a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8k0a_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8k0a_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8k0a_validation.xml.gz | 65.3 KB | Display | |
Data in CIF | 8k0a_validation.cif.gz | 95.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k0/8k0a ftp://data.pdbj.org/pub/pdb/validation_reports/k0/8k0a | HTTPS FTP |
-Related structure data
Related structure data | 36758MC 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 / Beg auth comp-ID: MET / Beg label comp-ID: MET
NCS ensembles :
NCS oper:
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-Components
#1: Protein | Mass: 51166.047 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: hcaE, digA, hcaA, hcaA1, phdC1, yfhU, b2538, JW2522 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P0ABR5, 3-phenylpropanoate dioxygenase #2: Protein | Mass: 20609.248 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: hcaF, digB, hcaA2, hcaB, phdC2, yfhV, b2539, JW2523 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q47140, 3-phenylpropanoate dioxygenase |
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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: Homohexamer of inositol phosphate phosphatase SopB / Type: COMPLEX / Entity ID: #1 / 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: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30478 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.7 Å2 | |||||||||||||||||||||||||||||||||||
Refine LS restraints |
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Refine LS restraints NCS |
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