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- PDB-8i51: Acyl-ACP synthetase structure bound to AMP-MC7 -

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Basic information

Entry
Database: PDB / ID: 8i51
TitleAcyl-ACP synthetase structure bound to AMP-MC7
ComponentsAcyl-acyl carrier protein synthetase
KeywordsCYTOSOLIC PROTEIN / Acyl-ACP synthetase / Tool enzyme
Function / homology
Function and homology information


: / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / 7-methoxy-7-oxidanylidene-heptanoic acid / Acyl-acyl carrier protein synthetase
Similarity search - Component
Biological speciesVibrio harveyi (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.76 Å
AuthorsHuang, H. / Wang, C. / Chang, S. / Cui, T. / Xu, Y. / Zhang, H. / Zhou, C. / Zhang, X. / Feng, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32125003 China
CitationJournal: To Be Published
Title: Acyl-ACP synthetase structure bound to AMP-MC7
Authors: Huang, H. / Wang, C. / Chang, S. / Cui, T. / Xu, Y. / Zhang, H. / Zhou, C. / Zhang, X. / Feng, Y.
History
DepositionJan 21, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Database references / Structure summary / Category: citation / struct / Item: _citation.title / _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acyl-acyl carrier protein synthetase
B: Acyl-acyl carrier protein synthetase
C: Acyl-acyl carrier protein synthetase
D: Acyl-acyl carrier protein synthetase
E: Acyl-acyl carrier protein synthetase
F: Acyl-acyl carrier protein synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)366,25224
Polymers362,9786
Non-polymers3,27418
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Acyl-acyl carrier protein synthetase / Long-chain fatty acid--CoA ligase


Mass: 60496.258 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio harveyi (bacteria) / Gene: aasS, AL538_21690 / Production host: Escherichia coli (E. coli) / References: UniProt: Q00IB3
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical
ChemComp-OP3 / 7-methoxy-7-oxidanylidene-heptanoic acid


Mass: 174.194 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H14O4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: Acyl-ACP Synthetase bound to AMP-MC7 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Vibrio harveyi (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 199919 / Symmetry type: POINT

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