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- PDB-5kof: Crosslinked Crystal Structure of Type II Fatty Acid Synthase Keto... -

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Basic information

Entry
Database: PDB / ID: 5kof
TitleCrosslinked Crystal Structure of Type II Fatty Acid Synthase Ketosynthase, FabB, and Acyl Carrier Protein, AcpP
Components
  • 3-oxoacyl-[acyl-carrier-protein] synthase 1
  • Acyl carrier protein
KeywordsTRANSFERASE / crosslinked / ketosynthase / ACP / complex
Function / homology
Function and homology information


monounsaturated fatty acid biosynthetic process / beta-ketoacyl-[acyl-carrier-protein] synthase I / lipid biosynthetic process / lipid A biosynthetic process / acyl binding / acyl carrier activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / response to xenobiotic stimulus ...monounsaturated fatty acid biosynthetic process / beta-ketoacyl-[acyl-carrier-protein] synthase I / lipid biosynthetic process / lipid A biosynthetic process / acyl binding / acyl carrier activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / response to xenobiotic stimulus / lipid binding / membrane / cytosol / cytoplasm
Similarity search - Function
Beta-ketoacyl synthase / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Beta-ketoacyl synthase / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain ...Beta-ketoacyl synthase / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Beta-ketoacyl synthase / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Acyl carrier protein (ACP) / Thiolase-like / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-6W5 / Acyl carrier protein / Acyl carrier protein / 3-oxoacyl-[acyl-carrier-protein] synthase 1 / 3-oxoacyl-[acyl-carrier-protein] synthase 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMilligan, J.C. / Jackson, D.R. / Barajas, J.F. / Tsai, S.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat.Chem.Biol. / Year: 2019
Title: Molecular basis for interactions between an acyl carrier protein and a ketosynthase.
Authors: Milligan, J.C. / Lee, D.J. / Jackson, D.R. / Schaub, A.J. / Beld, J. / Barajas, J.F. / Hale, J.J. / Luo, R. / Burkart, M.D. / Tsai, S.C.
History
DepositionJun 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: 3-oxoacyl-[acyl-carrier-protein] synthase 1
C: Acyl carrier protein
A: 3-oxoacyl-[acyl-carrier-protein] synthase 1
D: Acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,5366
Polymers102,7454
Non-polymers7912
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9660 Å2
ΔGint-49 kcal/mol
Surface area32260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.330, 103.920, 83.400
Angle α, β, γ (deg.)90.00, 110.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 3-oxoacyl-[acyl-carrier-protein] synthase 1 / 3-oxoacyl-[acyl-carrier-protein] synthase I / Beta-ketoacyl-ACP synthase I / KAS I


Mass: 42727.281 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-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P0A954, UniProt: P0A953*PLUS, 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-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: B7MJ81, UniProt: P0A6A8*PLUS
#3: Chemical ChemComp-6W5 / [(3~{S})-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-4-[[3-oxidanylidene-3-[2-(prop-2-enoylamino)ethylamino]propyl]amino]butyl] dihydrogen phosphate


Mass: 395.345 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H26N3O8P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O
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: 2.34 Å3/Da / Density % sol: 47.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.4
Details: 0.2 M Ammonium acetate, 0.1 M Sodium acetate pH 5.4, 20% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→48.978 Å / Num. obs: 37072 / % possible obs: 100 % / Redundancy: 2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.04978 / Rsym value: 0.0704 / Net I/σ(I): 7.27
Reflection shellResolution: 2.4→2.486 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.3953 / Mean I/σ(I) obs: 1.76 / CC1/2: 0.824 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(dev_2063: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VB9

2vb9


Resolution: 2.4→48.978 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.229 1993 5.38 %
Rwork0.2095 --
obs0.2105 37045 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→48.978 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7110 0 50 108 7268
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067262
X-RAY DIFFRACTIONf_angle_d1.5089810
X-RAY DIFFRACTIONf_dihedral_angle_d17.32623
X-RAY DIFFRACTIONf_chiral_restr0.0781117
X-RAY DIFFRACTIONf_plane_restr0.0061291
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.33771410.32752516X-RAY DIFFRACTION100
2.46-2.52660.32811400.3112477X-RAY DIFFRACTION100
2.5266-2.60090.29891430.29562496X-RAY DIFFRACTION100
2.6009-2.68480.27561410.28432485X-RAY DIFFRACTION100
2.6848-2.78080.31411380.272510X-RAY DIFFRACTION100
2.7808-2.89210.2891380.25762484X-RAY DIFFRACTION100
2.8921-3.02370.29291430.24722482X-RAY DIFFRACTION100
3.0237-3.18310.26341420.24492508X-RAY DIFFRACTION100
3.1831-3.38250.29081420.23612483X-RAY DIFFRACTION100
3.3825-3.64360.24871460.21492511X-RAY DIFFRACTION100
3.6436-4.01010.18831460.18682513X-RAY DIFFRACTION100
4.0101-4.590.18821440.16762512X-RAY DIFFRACTION100
4.59-5.78150.17691410.16342525X-RAY DIFFRACTION100
5.7815-48.98840.17191480.1582550X-RAY DIFFRACTION100

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