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- PDB-2wds: Crystal structure of the Streptomyces coelicolor H110A AcpS mutan... -

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Basic information

Entry
Database: PDB / ID: 2wds
TitleCrystal structure of the Streptomyces coelicolor H110A AcpS mutant in complex with cofactor CoA at 1.3 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
COENZYME A / Holo-[acyl-carrier-protein] synthase
Similarity search - Component
Biological speciesSTREPTOMYCES COELICOLOR (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 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 26, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 21, 2010Provider: 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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)15,4773
Polymers14,6851
Non-polymers7922
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)46,4309
Polymers44,0543
Non-polymers2,3766
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_455y-1/2,-z+1/2,-x1
crystal symmetry operation8_555-z,x+1/2,-y+1/21
Buried area8230 Å2
ΔGint-57 kcal/mol
Surface area15130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.719, 72.719, 72.719
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-2041-

HOH

21A-2050-

HOH

31A-2109-

HOH

41A-2110-

HOH

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Components

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


Mass: 14684.707 Da / Num. of mol.: 1 / Mutation: YES
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
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, HIS 110 TO ALA

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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: 0.3 M SODIUM ACETATE, 0.1 M SODIUM CACODYLATE PH 6.5, 25% PEG 2K MME WITH THE PRESENCE OF 10% PEG 400 AS CRYOPROTECTANT.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.117
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 30, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.117 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. obs: 28420 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 9.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 32
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 2.5 / % possible all: 99.3

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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: 1.35→51.43 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.954 / SU B: 0.842 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.205 1437 5.1 %RANDOM
Rwork0.183 ---
obs0.184 26745 99.3 %-
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: 18.97 Å2
Refinement stepCycle: LAST / Resolution: 1.35→51.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms882 0 49 237 1168
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.022996
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2292.0321376
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2755140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.68522.28635
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.56915149
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6431510
X-RAY DIFFRACTIONr_chiral_restr0.060.2160
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02740
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.180.2442
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2940.2697
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1190.2187
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2380.263
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0950.243
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2023647
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.86951001
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5136393
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.90610366
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: 1.35→1.39 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.307 104
Rwork0.285 1782

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