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- PDB-2jca: Crystal structure of the streptomyces coelicolor holo- [Acyl-carr... -

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Basic information

Entry
Database: PDB / ID: 2jca
TitleCrystal structure of the streptomyces coelicolor holo- [Acyl-carrier-protein] Synthase (AcpS) at 2 A.
ComponentsHOLO-[ACYL-CARRIER-PROTEIN] SYNTHASE
KeywordsTRANSFERASE / ACP / MAGNESIUM / POLIKETIDE / METAL-BINDING / LIPID SYNTHESIS / PHOSPHOPANTETHEINE ARM / FATTY ACID BIOSYNTHESIS / ACYL CARRIER PROTEIN SYNTHASE
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 speciesSTREPTOMYCES COELICOLOR (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsDall'Aglio, P. / Arthur, C. / Crump, M.P. / Crosby, J. / Hadfield, A.T.
CitationJournal: Biochemistry / Year: 2011
Title: Analysis of Streptomyces Coelicolor Phosphopantetheinyl Transferase, Acps, Reveals the Basis for Relaxed Substrate Specificity.
Authors: Dall'Aglio, P. / Arthur, C. / Williams, C. / Vasilakis, K. / Maple, H.J. / Crosby, J. / Crump, M.P. / Hadfield, A.T.
History
DepositionDec 21, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2007Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)44,6598
Polymers44,2553
Non-polymers4035
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-69.8 kcal/mol
Surface area15490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.940, 75.940, 108.351
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.2222, -0.274, 0.9357), (0.8421, -0.4297, -0.3258), (0.4914, 0.8604, 0.1352)26.09, -23.54, -18.19
2given(0.2454, 0.8683, 0.4312), (-0.2752, -0.3641, 0.8898), (0.9295, -0.337, 0.1496)22.75, 12.16, -29.6

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Components

#1: Protein HOLO-[ACYL-CARRIER-PROTEIN] SYNTHASE / HOLO-ACP SYNTHASE / 4'-PHOSPHOPANTETHEINYL TRANSFERASE ACPS / ACYL CARRIER PROTEIN SYNTHASE


Mass: 14751.777 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES COELICOLOR (bacteria) / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O86785, holo-[acyl-carrier-protein] synthase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.04 Å3/Da / Density % sol: 39.78 %
Crystal growpH: 8.8
Details: ACPS WAS DIALYZED IN 50 MM TRIS PH 8.8, 10% GLYCEROL. THEN IT WAS CRYSTALLIZED IN 0.2M AMMONIUM SULPHATE, 0.1M NACACODYLATE PH 6.5, 30% PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.48
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 23, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.48 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 25759 / % possible obs: 99.3 % / Redundancy: 6.4 % / Biso Wilson estimate: 29.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 22.19
Reflection shellResolution: 1.98→2.05 Å / Redundancy: 3 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.04 / % possible all: 95.7

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F7T

1f7t


Resolution: 1.98→65.8 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.791 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE ELECTRON DENSITY IN THE B CHAIN BETWEEN RESIDUES 65-68 IS NOT WELL DEFINED. THE ELECTRON DENSITY IN THE B CHAIN BETWEEN RESIDUES 22-25 IS NOT WELL DEFINED.
RfactorNum. reflection% reflectionSelection details
Rfree0.22 1305 5.1 %RANDOM
Rwork0.178 ---
obs0.18 24295 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20.13 Å20 Å2
2--0.26 Å20 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 1.98→65.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2661 0 22 199 2882
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222770
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.691.9783778
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.5195381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.12921.42998
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.14915424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0321530
X-RAY DIFFRACTIONr_chiral_restr0.1140.2446
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022075
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2170.21298
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.21939
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2188
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.275
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.210.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5521839
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.72632891
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.296972
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.20510880
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: 1.98→2.03 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.273 103
Rwork0.232 1683

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