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- PDB-5d3z: Crystal structure of the thioesterase domain of deoxyerythronolid... -

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Basic information

Entry
Database: PDB / ID: 5d3z
TitleCrystal structure of the thioesterase domain of deoxyerythronolide B synthase in complex with a small phosphonate inhibitor
ComponentsErythronolide synthase, modules 5 and 6
Keywordshydrolase/hydrolase inhibitor / Thioesterase domaine Alpha / beta hydrolase fold deoxyerythronolide B synthase Allyl phosphonate inhibitor / hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


6-deoxyerythronolide-B synthase / erythronolide synthase activity / macrolide biosynthetic process / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process
Similarity search - Function
Polyketide synthase, docking domain superfmaily / Polyketide synthase, thioesterase domain / Thioesterase / Polyketide synthase, docking domain / Erythronolide synthase docking domain / : / Polyketide synthase extender module SpnB, Rossmann fold domain / Thioesterase / Thioesterase domain / PKS_PP_betabranch ...Polyketide synthase, docking domain superfmaily / Polyketide synthase, thioesterase domain / Thioesterase / Polyketide synthase, docking domain / Erythronolide synthase docking domain / : / Polyketide synthase extender module SpnB, Rossmann fold domain / Thioesterase / Thioesterase domain / PKS_PP_betabranch / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / : / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / : / Acyl transferase/acyl hydrolase/lysophospholipase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / PKS_KR / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
prop-2-en-1-ylphosphonic acid / Erythronolide synthase EryA3
Similarity search - Component
Biological speciesSaccharopolyspora erythraea (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBergeret, F. / Argyropoulos, P. / Boddy, C.N. / Schmeing, T.M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP 106615 Canada
CitationJournal: Biochim.Biophys.Acta / Year: 2015
Title: Towards a characterization of the structural determinants of specificity in the macrocyclizing thioesterase for deoxyerythronolide B biosynthesis.
Authors: Argyropoulos, P. / Bergeret, F. / Pardin, C. / Reimer, J.M. / Pinto, A. / Boddy, C.N. / Schmeing, T.M.
History
DepositionAug 6, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2016Group: Database references
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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_symmetry / _struct_conn_type.id
Revision 2.0Dec 25, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / pdbx_entry_details ...atom_site / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_conn_type / struct_site_gen
Item: _atom_site.auth_seq_id / _pdbx_nonpoly_scheme.pdb_seq_num ..._atom_site.auth_seq_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_site_gen.auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Erythronolide synthase, modules 5 and 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1824
Polymers28,7811
Non-polymers4003
Water3,765209
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.544, 112.544, 42.780
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321

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Components

#1: Protein Erythronolide synthase, modules 5 and 6 / 6-deoxyerythronolide B synthase III / DEBS 3 / ORF 3


Mass: 28781.148 Da / Num. of mol.: 1 / Fragment: unp residues 2904-3172
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharopolyspora erythraea (bacteria) / Gene: eryA / Plasmid: pBacP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3
References: UniProt: Q03133, 6-deoxyerythronolide-B synthase
#2: Chemical ChemComp-57H / prop-2-en-1-ylphosphonic acid


Mass: 122.060 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7O3P
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.72 Å3/Da / Density % sol: 54.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM Na-cacodylate, 35-38% polyethylene glycol (PEG) 300, 0.18-0.24 M Ca-acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 2, 2012 / Details: Rigaku Varimax-HF
RadiationMonochromator: Rigaku Varimax-HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→32.15 Å / Num. obs: 18469 / % possible obs: 99.6 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.12 / Rsym value: 0.12 / Net I/σ(I): 20.5
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 6.9 / % possible all: 98.4

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Processing

Software
NameVersionClassification
HKL-2000706data scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.15data extraction
HKL-2000706data reduction
PHASER2.5.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KEZ

1kez


Resolution: 2.1→32.15 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.298 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.184 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1904 932 5.1 %RANDOM
Rwork0.1699 ---
obs0.171 17518 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 53.68 Å2 / Biso mean: 17.466 Å2 / Biso min: 7.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0.05 Å2-0 Å2
2---0.09 Å20 Å2
3---0.3 Å2
Refinement stepCycle: final / Resolution: 2.1→32.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1964 0 21 210 2195
Biso mean--34.68 27.76 -
Num. residues----263
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192055
X-RAY DIFFRACTIONr_bond_other_d0.0010.021889
X-RAY DIFFRACTIONr_angle_refined_deg1.1441.9612807
X-RAY DIFFRACTIONr_angle_other_deg0.75734341
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9025267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.0522.70685
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.44115283
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0891517
X-RAY DIFFRACTIONr_chiral_restr0.0590.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212362
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02463
X-RAY DIFFRACTIONr_mcbond_it0.8771.6281065
X-RAY DIFFRACTIONr_mcbond_other0.8471.6261064
X-RAY DIFFRACTIONr_mcangle_it1.4762.4331333
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.144 73 -
Rwork0.154 1267 -
all-1340 -
obs--99.63 %

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