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- PDB-5d3k: Crystal structure of the thioesterase domain of deoxyerythronolid... -

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Basic information

Entry
Database: PDB / ID: 5d3k
TitleCrystal structure of the thioesterase domain of deoxyerythronolide B synthase
ComponentsErythronolide synthase, modules 5 and 6
KeywordsHYDROLASE / Thioesterase domaine Alpha / beta hydrolase fold deoxyerythronolide B synthase
Function / homology
Function and homology information


6-deoxyerythronolide-B synthase / erythronolide synthase activity / macrolide biosynthetic process / DIM/DIP cell wall layer assembly / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / plasma membrane / cytoplasm
Similarity search - Function
Polyketide synthase, docking domain superfmaily / Polyketide synthase, thioesterase domain / Thioesterase / Polyketide synthase, docking domain / Erythronolide synthase docking domain / Thioesterase / Thioesterase domain / Polyketide synthase, C-terminal extension / PKS_PP_betabranch / Ketoacyl-synthetase C-terminal extension ...Polyketide synthase, docking domain superfmaily / Polyketide synthase, thioesterase domain / Thioesterase / Polyketide synthase, docking domain / Erythronolide synthase docking domain / Thioesterase / Thioesterase domain / Polyketide synthase, C-terminal extension / PKS_PP_betabranch / 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 / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / PKS_KR / Ketosynthase family 3 (KS3) domain profile. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / 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
6-deoxyerythronolide-B synthase EryA3, modules 5 and 6
Similarity search - Component
Biological speciesSaccharopolyspora erythraea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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
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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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.pdbx_dist_value / _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

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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)29,3786
Polymers28,7811
Non-polymers5975
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)112.920, 112.920, 42.970
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-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.75 Å3/Da / Density % sol: 55.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM Na-cacodylate, 35-38% polyethylene glycol , 0.18-0.24 M Ca-acetate, PEG300

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.97957 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Feb 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97957 Å / Relative weight: 1
ReflectionResolution: 1.7→36.96 Å / Num. all: 34562 / Num. obs: 34562 / % possible obs: 99.1 % / Redundancy: 4.1 % / CC1/2: 0.992 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.062 / Rrim(I) all: 0.136 / Rsym value: 0.12 / Net I/σ(I): 7.3 / Num. measured all: 140978
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRsym value% possible all
1.7-1.7940.4782.82031850640.7740.0350.069100
5.38-36.964.20.06913.4455010760.9930.0410.08391.1

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Processing

Software
NameVersionClassification
SCALA3.3.21data scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
REFMAC5.8.0073phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KEZ

1kez


Resolution: 1.7→36.96 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.758 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1866 1638 4.7 %RANDOM
Rwork0.1563 ---
obs0.1577 32914 99.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 62.6 Å2 / Biso mean: 17.054 Å2 / Biso min: 7.16 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å20 Å2
3----0.04 Å2
Refinement stepCycle: final / Resolution: 1.7→36.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2006 0 32 226 2264
Biso mean--43.5 29.48 -
Num. residues----269
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0192101
X-RAY DIFFRACTIONr_bond_other_d0.0010.021929
X-RAY DIFFRACTIONr_angle_refined_deg1.9951.9612865
X-RAY DIFFRACTIONr_angle_other_deg0.96434437
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3955272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.52222.77890
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.58915285
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6451518
X-RAY DIFFRACTIONr_chiral_restr0.1320.2310
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212422
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02478
X-RAY DIFFRACTIONr_mcbond_it1.7651.4131084
X-RAY DIFFRACTIONr_mcbond_other1.7591.4121084
X-RAY DIFFRACTIONr_mcangle_it2.5772.1091357
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 113 -
Rwork0.225 2436 -
all-2549 -
obs--99.96 %

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