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- PDB-7sqi: Crosslinked Crystal Structure of Type II Fatty Acid Synthase Keto... -

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Basic information

Entry
Database: PDB / ID: 7sqi
TitleCrosslinked Crystal Structure of Type II Fatty Acid Synthase Ketosynthase, FabB, and C14-crypto Acyl Carrier Protein, AcpP
Components
  • Acyl carrier protein
  • Beta-ketoacyl-ACP synthase I
KeywordsTRANSFERASE / ketosynthase / crosslink / FabB / ACP / KASI
Function / homology
Function and homology information


lipid A biosynthetic process / acyl binding / acyl carrier activity / membrane / cytosol
Similarity search - Function
ACP-like / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Acyl carrier protein (ACP) / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-A7V / : / Acyl carrier protein
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsChen, A. / Mindrebo, J.T. / Davis, T.D. / Noel, J.P. / Burkart, M.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM097907 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Mechanism-based cross-linking probes capture the Escherichia coli ketosynthase FabB in conformationally distinct catalytic states.
Authors: Chen, A. / Mindrebo, J.T. / Davis, T.D. / Kim, W.E. / Katsuyama, Y. / Jiang, Z. / Ohnishi, Y. / Noel, J.P. / Burkart, M.D.
History
DepositionNov 5, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-ketoacyl-ACP synthase I
B: Beta-ketoacyl-ACP synthase I
C: Acyl carrier protein
D: Acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,5878
Polymers102,3734
Non-polymers1,2144
Water19,2581069
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10750 Å2
ΔGint-55 kcal/mol
Surface area30560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.990, 112.380, 141.640
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-ketoacyl-ACP synthase I


Mass: 42541.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: fabB, FAZ83_00695 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A6D2VX38, beta-ketoacyl-[acyl-carrier-protein] synthase I
#2: Protein Acyl carrier protein / ACP


Mass: 8645.460 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B7MJ81
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-A7V / N-{2-[(2Z)-3-chlorotetradec-2-enamido]ethyl}-N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alaninamide


Mass: 584.083 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H47ClN3O8P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1069 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.36 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 8000, 0.3 M sodium acetate, 0.1 M sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→39.1 Å / Num. obs: 104223 / % possible obs: 99.68 % / Redundancy: 12 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.342 / Rpim(I) all: 0.102 / Rrim(I) all: 0.357 / Net I/σ(I): 527
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsRpim(I) allRrim(I) allΧ2% possible all
1.7-1.7311.95.72551041.7065.9810.8599.5
9.31-39.112.60.0577440.0160.0590.6898.8

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Processing

Software
NameVersionClassification
PHENIX1.19.2refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6okc

6okc


Resolution: 1.7→39.1 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.2052 --
Rwork0.1709 --
obs-104223 99.68 %
Displacement parametersBiso max: 120.72 Å2 / Biso mean: 23.8032 Å2 / Biso min: 7.79 Å2
Refinement stepCycle: LAST / Resolution: 1.7→39.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7004 0 74 1069 8147
LS refinement shellResolution: 1.7→1.761 Å /
Rfactor% reflection
Rfree0.3285 -
Rwork0.3086 -
obs-98.55 %

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