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- PDB-2wdo: Crystal structure of the S. coelicolor AcpS in complex with acety... -

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Basic information

Entry
Database: PDB / ID: 2wdo
TitleCrystal structure of the S. coelicolor AcpS in complex with acetyl- CoA at 1.5 A
ComponentsHOLO-[ACYL-CARRIER-PROTEIN] SYNTHASE
KeywordsTRANSFERASE / PHOSPHOPANTETHEINE ARM / FATTY ACID BIOSYNTHESIS / LIPID SYNTHESIS / POLYKETIDES
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
ACETYL COENZYME *A / COENZYME A / Holo-[acyl-carrier-protein] synthase
Similarity search - Component
Biological speciesSTREPTOMYCES COELICOLOR (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 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
DepositionMar 25, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2011Group: Atomic model / Database references ...Atomic model / 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_conn / 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5416
Polymers14,7521
Non-polymers1,7905
Water4,270237
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)49,62418
Polymers44,2553
Non-polymers5,36915
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_545-y,z-1/2,-x+1/21
crystal symmetry operation7_555-z+1/2,-x,y+1/21
Buried area13370 Å2
ΔGint-111.9 kcal/mol
Surface area13970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.833, 72.833, 72.833
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-1127-

GOL

21A-1127-

GOL

31A-1128-

SO4

41A-1128-

SO4

51A-2096-

HOH

61A-2117-

HOH

71A-2119-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 14751.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ACETYL-COA AND COA ARE PRESENT IN THE ACTIVE SITE / Source: (gene. exp.) STREPTOMYCES COELICOLOR (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O86785, holo-[acyl-carrier-protein] synthase

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Non-polymers , 6 types, 242 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ACO / ACETYL COENZYME *A / Acetyl-CoA


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#4: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsCOENZYME A (COA): PRESENT AS CONTAMINATION

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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: 2.2 Å3/Da / Density % sol: 44 % / Description: NONE
Crystal growpH: 6.5
Details: 0.2 M LITHIUM SULPHATE, 25% PEG 2K MME, 0.1 M SODIUM CACODYLATE PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.953
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953 Å / Relative weight: 1
ReflectionResolution: 1.56→50 Å / Num. obs: 18659 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 9.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 32
Reflection shellResolution: 1.56→1.62 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JBZ

2jbz


Resolution: 1.56→51.5 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.939 / SU B: 1.896 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. INSPECTION OF THE ELECTRON DENSITY IN THE ACETYL-COA REGION, INITIALLY REFINED WITH A FULL OCCUPANCY COFACTOR, AND THE FACT THAT THE ACETYL- ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. INSPECTION OF THE ELECTRON DENSITY IN THE ACETYL-COA REGION, INITIALLY REFINED WITH A FULL OCCUPANCY COFACTOR, AND THE FACT THAT THE ACETYL-COA STOCK CONTAINED A CONTAMINATION OF THE STANDARD COFACTOR, SUGGESTED THE ADDITIONAL PRESENCE OF COA
RfactorNum. reflection% reflectionSelection details
Rfree0.232 956 5.1 %RANDOM
Rwork0.202 ---
obs0.204 17671 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.18 Å2
Refinement stepCycle: LAST / Resolution: 1.56→51.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms887 0 111 237 1235
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211084
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5332.0881498
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2635142
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.38522.43237
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.11815152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2341510
X-RAY DIFFRACTIONr_chiral_restr0.0910.2166
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02785
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2110.2482
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2950.2731
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2380.2203
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.286
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2610.249
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6713662
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.42651021
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.8546477
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.87210469
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: 1.56→1.6 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 77 -
Rwork0.22 1271 -
obs--100 %

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