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

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Basic information

Entry
Database: PDB / ID: 5cmo
TitleCrystal structure of holo-[acyl-carrier-protein] synthase (AcpS) from Neisseria meningitidis
ComponentsHolo-[acyl-carrier-protein] synthase
KeywordsTRANSFERASE / acpS / FASII / trimer
Function / homology
Function and homology information


holo-[acyl-carrier-protein] synthase / holo-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / 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 speciesNeisseria meningitidis serogroup C / serotype 2a
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNanson, J.D. / Forwood, J.K.
CitationJournal: To Be Published
Title: Crystal structure of holo-[acyl-carrier-protein] synthase (AcpS) from Neisseria meningitidis
Authors: Nanson, J.D. / Forwood, J.K.
History
DepositionJul 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Data collection / Derived calculations / Refinement description
Category: diffrn_source / pdbx_struct_oper_list / software
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)41,1774
Polymers41,0853
Non-polymers921
Water4,774265
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-23 kcal/mol
Surface area17520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.064, 90.073, 93.045
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 13694.843 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis serogroup C / serotype 2a (strain ATCC 700532 / DSM 15464 / FAM18) (bacteria)
Strain: ATCC 700532 / DSM 15464 / FAM18 / Gene: acpS, NMC1700 / Plasmid: pMCSG21 / Production host: Escherichia coli (E. coli)
References: UniProt: A1KVH5, holo-[acyl-carrier-protein] synthase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.82 %
Crystal growTemperature: 296.15 K / Method: vapor diffusion, hanging drop / Details: 200 mM sodium citrate tribasic, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→48.06 Å / Num. obs: 28036 / % possible obs: 100 % / Redundancy: 7.2 % / Net I/σ(I): 9.1
Reflection shellResolution: 2→2.05 Å / Redundancy: 7 % / Mean I/σ(I) obs: 3.4 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIXdev_1834refinement
XDSdata scaling
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→46.522 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2224 1385 4.95 %
Rwork0.1948 --
obs0.1962 27982 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→46.522 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2898 0 6 265 3169
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042960
X-RAY DIFFRACTIONf_angle_d0.8373977
X-RAY DIFFRACTIONf_dihedral_angle_d13.0481097
X-RAY DIFFRACTIONf_chiral_restr0.034435
X-RAY DIFFRACTIONf_plane_restr0.003510
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.07150.29691230.25142595X-RAY DIFFRACTION100
2.0715-2.15450.26931560.22922597X-RAY DIFFRACTION100
2.1545-2.25250.22541450.22892593X-RAY DIFFRACTION100
2.2525-2.37130.26411390.20762642X-RAY DIFFRACTION100
2.3713-2.51980.24491330.22462645X-RAY DIFFRACTION100
2.5198-2.71440.25981200.22712649X-RAY DIFFRACTION100
2.7144-2.98750.28561450.21542666X-RAY DIFFRACTION100
2.9875-3.41960.23411400.19412663X-RAY DIFFRACTION100
3.4196-4.30790.18621230.16372726X-RAY DIFFRACTION100
4.3079-46.53510.17211610.16892821X-RAY DIFFRACTION100

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