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- PDB-5vbx: Crystal structure of holo-[acyl-carrier-protein] synthase (AcpS) ... -

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Basic information

Entry
Database: PDB / ID: 5vbx
TitleCrystal structure of holo-[acyl-carrier-protein] synthase (AcpS) from Escherichia coli
ComponentsHolo-[acyl-carrier-protein] synthase
KeywordsTRANSFERASE / Trimer
Function / homology
Function and homology information


holo-[acyl-carrier-protein] synthase / holo-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / transferase activity / magnesium ion binding / cytoplasm
Similarity search - Function
4'-phosphopantetheinyl transferase domain / Holo-[acyl carrier protein] synthase / Phosphopantetheine-protein transferase domain / 4'-phosphopantetheinyl transferase domain / 4'-phosphopantetheinyl transferase domain superfamily / 4'-phosphopantetheinyl transferase superfamily / Ribosomal Protein L22; Chain A / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Holo-[acyl-carrier-protein] synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsMarcella, A.M. / Barb, A.W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)EEC-0813570 United States
Argonne National Laboratory (Beam time)GUP-48455 United States
CitationJournal: J. Mol. Biol. / Year: 2017
Title: Structure, High Affinity, and Negative Cooperativity of the Escherichia coli Holo-(Acyl Carrier Protein):Holo-(Acyl Carrier Protein) Synthase Complex.
Authors: Marcella, A.M. / Culbertson, S.J. / Shogren-Knaak, M.A. / Barb, A.W.
History
DepositionMar 30, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 9, 2019Group: Data collection / Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Holo-[acyl-carrier-protein] synthase
B: Holo-[acyl-carrier-protein] synthase
C: Holo-[acyl-carrier-protein] synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,92620
Polymers42,2233
Non-polymers70317
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7830 Å2
ΔGint-127 kcal/mol
Surface area16690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.376, 69.522, 59.894
Angle α, β, γ (deg.)90.00, 109.55, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-364-

HOH

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Components

#1: Protein Holo-[acyl-carrier-protein] synthase / Holo-ACP synthase / 4'-phosphopantetheinyl transferase AcpS


Mass: 14074.297 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: acpS, dpj, b2563, JW2547 / Production host: Escherichia coli (E. coli)
References: UniProt: P24224, holo-[acyl-carrier-protein] synthase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O

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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: 2.33 Å3/Da / Density % sol: 47.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.8-2.2 M Sodium Formate 1.8-2.2 M Sodium Nitrate 100 mM HEPES pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.003 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.003 Å / Relative weight: 1
ReflectionResolution: 2.05→29.598 Å / Num. obs: 24465 / % possible obs: 100 % / Redundancy: 4.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.1458 / Net I/σ(I): 10.24
Reflection shellHighest resolution: 2.05 Å / Redundancy: 3.9 % / Num. unique obs: 2704 / CC1/2: 0.538 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F7T

1f7t


Resolution: 2.05→29.598 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 25.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2424 1138 4.65 %RANDOM
Rwork0.1916 ---
obs0.194 24465 99.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→29.598 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2903 0 41 156 3100
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073002
X-RAY DIFFRACTIONf_angle_d0.9684047
X-RAY DIFFRACTIONf_dihedral_angle_d17.2181781
X-RAY DIFFRACTIONf_chiral_restr0.058459
X-RAY DIFFRACTIONf_plane_restr0.006515
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.14330.32081380.26772912X-RAY DIFFRACTION100
2.1433-2.25620.29681330.24542895X-RAY DIFFRACTION100
2.2562-2.39750.34331240.23892911X-RAY DIFFRACTION100
2.3975-2.58260.28021460.22512899X-RAY DIFFRACTION100
2.5826-2.84230.29461670.21972883X-RAY DIFFRACTION100
2.8423-3.25310.26831470.19842905X-RAY DIFFRACTION100
3.2531-4.09680.18691480.15852931X-RAY DIFFRACTION100
4.0968-29.60090.18931350.1552991X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 127.6352 Å / Origin y: -9.4766 Å / Origin z: 245.3615 Å
111213212223313233
T0.2494 Å20.0156 Å2-0.0325 Å2-0.1544 Å20.0168 Å2--0.1521 Å2
L1.1274 °20.2505 °20.2619 °2-1.371 °20.3096 °2--1.3035 °2
S0.0584 Å °0.0668 Å °0.0434 Å °0.1001 Å °-0.0353 Å °-0.0318 Å °-0.0186 Å °0.0219 Å °-0.0422 Å °
Refinement TLS groupSelection details: all

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