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- PDB-5xuk: Crystal structure of Helicobacter pylori holo-[acyl-carrier-prote... -

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Basic information

Entry
Database: PDB / ID: 5xuk
TitleCrystal structure of Helicobacter pylori holo-[acyl-carrier-protein] synthase (AcpS) in complex with coenzyme A
ComponentsHolo-[acyl-carrier-protein] synthase
KeywordsTRANSFERASE / Gram-negative bacteria / phosphopantetheinyl transferase / homotrimer
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
COENZYME A / Holo-[acyl-carrier-protein] synthase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLiao, Y.P. / Wang, D.L. / Yin, D.P. / Zhang, Q.Y. / Wang, Y.M. / Wang, D.Q. / Zhu, H.X. / Chen, S.
CitationJournal: To Be Published
Title: Crystal structures of acyl carrier protein synthases (AcpS) from three Gram-negative bacteria
Authors: Liao, Y.P. / Wang, D.L. / Yin, D.P. / Zhang, Q.Y. / Wang, Y.M. / Wang, D.Q. / Zhu, H.X. / Chen, S.
History
DepositionJun 23, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7902
Polymers13,0221
Non-polymers7681
Water48627
1
A: Holo-[acyl-carrier-protein] synthase
hetero molecules

A: Holo-[acyl-carrier-protein] synthase
hetero molecules

A: Holo-[acyl-carrier-protein] synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3706
Polymers39,0673
Non-polymers2,3033
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area7020 Å2
ΔGint-35 kcal/mol
Surface area15890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.340, 93.340, 43.020
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

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


Mass: 13022.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (strain ATCC 700392 / 26695) (bacteria)
Strain: ATCC 700392 / 26695 / Gene: acpS, HP_0808 / Production host: Escherichia coli (E. coli)
References: UniProt: O25488, holo-[acyl-carrier-protein] synthase
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 4.15 Å3/Da / Density % sol: 70.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 28% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→46.67 Å / Num. obs: 9185 / % possible obs: 94 % / Redundancy: 4.1 % / Biso Wilson estimate: 50.24 Å2 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.034 / Net I/σ(I): 11.1
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 4 % / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 1282 / Rpim(I) all: 0.217 / % possible all: 91.4

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HYK

3hyk


Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.923 / SU B: 6.309 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.239 / ESU R Free: 0.219 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27709 442 4.8 %RANDOM
Rwork0.22786 ---
obs0.23014 8722 93.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 55.11 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å2-0.37 Å20 Å2
2---0.73 Å20 Å2
3---1.1 Å2
Refinement stepCycle: 1 / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms881 0 40 27 948
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.019935
X-RAY DIFFRACTIONr_bond_other_d0.0010.02650
X-RAY DIFFRACTIONr_angle_refined_deg1.3742.0431260
X-RAY DIFFRACTIONr_angle_other_deg0.8131604
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5015114
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.61124.28628
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.78215183
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.091153
X-RAY DIFFRACTIONr_chiral_restr0.0750.2149
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02963
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02175
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 35 -
Rwork0.331 577 -
obs--90.67 %

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