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- PDB-2wdy: Crystal structure of the Streptomyces coelicolor D111A AcpS mutan... -

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Basic information

Entry
Database: PDB / ID: 2wdy
TitleCrystal structure of the Streptomyces coelicolor D111A AcpS mutant in complex with cofactor CoA at 1.4 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: 1.4 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 27, 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 / 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.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: HOLO-[ACYL-CARRIER-PROTEIN] SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5475
Polymers14,7081
Non-polymers8394
Water3,729207
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)46,64115
Polymers44,1233
Non-polymers2,51712
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 area8020 Å2
ΔGint-98.6 kcal/mol
Surface area15590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.831, 72.831, 72.831
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-

NA

21A-2011-

HOH

31A-2031-

HOH

41A-2080-

HOH

51A-2081-

HOH

61A-2092-

HOH

71A-2167-

HOH

81A-2198-

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: 14707.768 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: MG AND COA ARE PRESENT IN THE ACTIVE SITE. INSPECTION OF THE ELECTRON DENSITY SUGGESTS COA BINDS IN 2 ALTERNATIVE CONFORMATIONS.
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-COA / COENZYME A


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


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 111 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: 0.2 M POTASSIUM THIOCYANATE, 0.1 M SODIUM CACODYLATE PH 6.5, 8% PEG 20K PLUS 8% PEG 550 MME, 15% GLYCEROL WAS THEN ADDED AS CRYO

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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 / Date: Feb 11, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 25707 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 7.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 34.7
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.5 / % possible all: 96.4

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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: 1.4→51.5 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.096 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. COA WAS BOUND IN TWO ALTERNATIVE CONFORMATIONS. WHILST THE ELECTRON DENSITY FOR THE ADENINE RINGS OF BOTH COAS, INCLUDING THE PHOSPHATES, ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. COA WAS BOUND IN TWO ALTERNATIVE CONFORMATIONS. WHILST THE ELECTRON DENSITY FOR THE ADENINE RINGS OF BOTH COAS, INCLUDING THE PHOSPHATES, AND THEIR RELATED MAGNESIUM IONS WAS VERY CLEAR, THE DENSITY FOR THE PHOSPHOPANTETHEINE ARMS WAS NOT WELL DEFINED
RfactorNum. reflection% reflectionSelection details
Rfree0.21498 1311 5.1 %RANDOM
Rwork0.18875 ---
obs0.19011 24241 99.52 %-
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: 21.166 Å2
Refinement stepCycle: LAST / Resolution: 1.4→51.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms884 0 51 207 1142
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0211088
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2712.0671514
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1085147
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.58522.05139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.69715157
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8851511
X-RAY DIFFRACTIONr_chiral_restr0.0680.2167
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02802
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1930.2479
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2920.2747
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.2162
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.160.254
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.264
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2523646
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.15451029
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.526462
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.71110473
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: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 97 -
Rwork0.296 1722 -
obs--96.24 %

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