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- PDB-8sms: Crosslinked Crystal Structure of Type II Fatty Acid Synthase, Fab... -

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Basic information

Entry
Database: PDB / ID: 8sms
TitleCrosslinked Crystal Structure of Type II Fatty Acid Synthase, FabB, and cerulenin crosslinker-crypto Acyl Carrier Protein, AcpP
Components
  • 3-oxoacyl-[acyl-carrier-protein] synthase 1
  • Acyl carrier protein
KeywordsBIOSYNTHETIC PROTEIN / Ketosynthase / FabB / AcpP / acyl carrier protein / cerulenin / crosslinker / crosslink / fatty acid biosynthesis / natural product
Function / homology
Function and homology information


Kdo2-lipid A biosynthetic process / monounsaturated fatty acid biosynthetic process / beta-ketoacyl-[acyl-carrier-protein] synthase I / lipid A biosynthetic process / acyl binding / acyl carrier activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / cytosol
Similarity search - Function
Beta-ketoacyl synthase / 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 ...Beta-ketoacyl synthase / 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
Similarity search - Domain/homology
Chem-G7U / Acyl carrier protein / 3-oxoacyl-[acyl-carrier-protein] synthase 1
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Atlantibacter hermannii NBRC 105704 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsJiang, Z. / Chen, A. / Chen, J. / Sekhon, A. / Louie, G.V. / Noel, J.P. / La Clair, J.J. / Burkart, M.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Chem Sci / Year: 2023
Title: Masked cerulenin enables a dual-site selective protein crosslink.
Authors: Jiang, Z. / Chen, A. / Chen, J. / Sekhon, A. / Louie, G.V. / Noel, J.P. / La Clair, J.J. / Burkart, M.D.
History
DepositionApr 26, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._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_author.identifier_ORCID
Revision 1.2Oct 23, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)103,3286
Polymers102,2214
Non-polymers1,1072
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10560 Å2
ΔGint-56 kcal/mol
Surface area31520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.030, 100.230, 78.310
Angle α, β, γ (deg.)90.00, 109.34, 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: 42596.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: fabB, fabC, b2323, JW2320
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P0A953, beta-ketoacyl-[acyl-carrier-protein] synthase I
#2: Protein Acyl carrier protein


Mass: 8514.264 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Atlantibacter hermannii NBRC 105704 (bacteria)
Gene: acpP
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: H5V184
#3: Chemical ChemComp-G7U / N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-{2-[(2R)-2-hydroxy-4-oxododecanamido]ethyl}-beta-alaninamide


Mass: 553.583 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H44N3O10P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.14 Å3/Da / Density % sol: 42.48 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop
Details: 26% PEG 8000, 0.3M sodium acetate, 0.1 M sodium cacodylate pH 6.0,

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 18, 2023
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.93→37.25 Å / Num. obs: 63659 / % possible obs: 98.6 % / Redundancy: 6 % / CC1/2: 0.994 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.076 / Rrim(I) all: 0.188 / Χ2: 0.98 / Net I/σ(I): 7.7 / Num. measured all: 384446
Reflection shellResolution: 1.93→1.98 Å / % possible obs: 97.1 % / Redundancy: 5.4 % / Rmerge(I) obs: 1.381 / Num. measured all: 22988 / Num. unique obs: 4228 / CC1/2: 0.65 / Rpim(I) all: 0.64 / Rrim(I) all: 1.527 / Χ2: 0.97 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→37.25 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 28.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2551 3057 4.8 %
Rwork0.2016 --
obs0.2042 63627 98.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.93→37.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7131 0 72 248 7451
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d1.046
X-RAY DIFFRACTIONf_dihedral_angle_d7.1931097
X-RAY DIFFRACTIONf_chiral_restr0.061140
X-RAY DIFFRACTIONf_plane_restr0.0091331
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.960.36171190.3162718X-RAY DIFFRACTION96
1.96-1.990.36351470.29882705X-RAY DIFFRACTION99
1.99-2.030.36021230.29062785X-RAY DIFFRACTION99
2.03-2.060.3311590.2782725X-RAY DIFFRACTION99
2.06-2.10.33991630.28652733X-RAY DIFFRACTION99
2.1-2.150.35911460.26662750X-RAY DIFFRACTION99
2.15-2.190.30481500.26072760X-RAY DIFFRACTION99
2.19-2.240.33291490.25442710X-RAY DIFFRACTION98
2.24-2.30.30541420.25442690X-RAY DIFFRACTION97
2.3-2.360.29921190.23582779X-RAY DIFFRACTION99
2.36-2.430.30991370.23512761X-RAY DIFFRACTION99
2.43-2.510.28571540.22472751X-RAY DIFFRACTION99
2.51-2.60.29861150.21282759X-RAY DIFFRACTION99
2.6-2.70.28971510.20962768X-RAY DIFFRACTION98
2.7-2.830.281170.21972710X-RAY DIFFRACTION97
2.83-2.980.27521580.2042771X-RAY DIFFRACTION99
2.98-3.160.23111310.18992773X-RAY DIFFRACTION99
3.16-3.410.24541350.18332764X-RAY DIFFRACTION99
3.41-3.750.24491310.17322767X-RAY DIFFRACTION98
3.75-4.290.18371220.1462820X-RAY DIFFRACTION99
4.29-5.40.15991610.13872725X-RAY DIFFRACTION98
5.4-37.250.18431280.16072846X-RAY DIFFRACTION99

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