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- PDB-3el6: Crystal Structure of the Erythromycin Dehydratase -

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Basic information

Entry
Database: PDB / ID: 3el6
TitleCrystal Structure of the Erythromycin Dehydratase
ComponentsErythromycin dehydratase
KeywordsLYASE / Dehydratase Double hotdog fold Cis-proline / Acyltransferase / Antibiotic biosynthesis / Multifunctional enzyme / NADP / Phosphopantetheine / Transferase
Function / homology
Function and homology information


6-deoxyerythronolide-B synthase / erythronolide synthase activity / macrolide biosynthetic process / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / oxidoreductase activity
Similarity search - Function
Erythronolide synthase, docking / Erythronolide synthase, docking domain superfamily / Erythronolide synthase, docking / Polyketide synthase dehydratase / Zinc-binding dehydrogenase / Polyketide synthase, docking domain / Erythronolide synthase docking domain / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / : / : ...Erythronolide synthase, docking / Erythronolide synthase, docking domain superfamily / Erythronolide synthase, docking / Polyketide synthase dehydratase / Zinc-binding dehydrogenase / Polyketide synthase, docking domain / Erythronolide synthase docking domain / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / : / : / Polyketide synthase dehydratase domain / PKS_PP_betabranch / Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain / KR domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Thiol Ester Dehydrase; Chain A / Malonyl-CoA ACP transacylase, ACP-binding / PKS_KR / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / Ketosynthase family 3 (KS3) domain profile. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / 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 / GroES-like superfamily / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Thiolase-like / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
6-deoxyerythronolide-B synthase EryA2, modules 3 and 4
Similarity search - Component
Biological speciesSaccharopolyspora erythraea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsKeatinge-Clay, A.T.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Crystal structure of the erythromycin polyketide synthase dehydratase.
Authors: Keatinge-Clay, A.
History
DepositionSep 20, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Erythromycin dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8493
Polymers32,7171
Non-polymers1322
Water4,450247
1
A: Erythromycin dehydratase
hetero molecules

A: Erythromycin dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6986
Polymers65,4352
Non-polymers2634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2240 Å2
ΔGint-15 kcal/mol
Surface area22740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.997, 66.997, 186.238
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Erythromycin dehydratase / ORF 2 / 6-deoxyerythronolide B synthase II / DEBS 2


Mass: 32717.383 Da / Num. of mol.: 1 / Fragment: EryDH4 (UNP residues 2362 to 2653)
Source method: isolated from a genetically manipulated source
Details: DNA inserted between NdeI and XhoI sites / Source: (gene. exp.) Saccharopolyspora erythraea (bacteria) / Gene: eryA / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q03132, EC: 4.2.1.61
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 3.19 Å3/Da / Density % sol: 61.49 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 2.15 M ammonium sulfate, 100 mM sodium cacodylate pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159, 0.9200
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 12, 2008 / Details: mirrors
RadiationMonochromator: Mirrors at ALS BL8.3.1 that tuned the synchrotron radiation
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.11591
20.921
ReflectionResolution: 1.85→50 Å / Num. all: 37089 / Num. obs: 37089 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 42.5
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 14.2 % / Rmerge(I) obs: 0.659 / Mean I/σ(I) obs: 2.5 / Num. unique all: 3513 / Rsym value: 0.659 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
REFMAC5.4.0067refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: A model generated by PHENIX from the anomalous bromine dataset

Resolution: 1.85→45.55 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.492 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.115 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22692 3687 10 %RANDOM
Rwork0.19722 ---
obs0.2003 33313 99.86 %-
all-37089 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.98 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20 Å20 Å2
2--0.35 Å20 Å2
3----0.69 Å2
Refinement stepCycle: LAST / Resolution: 1.85→45.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1989 0 6 247 2242
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0212036
X-RAY DIFFRACTIONr_angle_refined_deg1.7941.9652792
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0125269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.72485
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.83915283
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3711514
X-RAY DIFFRACTIONr_chiral_restr0.1480.2326
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211578
X-RAY DIFFRACTIONr_mcbond_it1.4091.51343
X-RAY DIFFRACTIONr_mcangle_it2.54922136
X-RAY DIFFRACTIONr_scbond_it3.3973693
X-RAY DIFFRACTIONr_scangle_it5.6354.5656
LS refinement shellResolution: 1.853→1.901 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 259 -
Rwork0.267 2368 -
obs-2621 98.57 %

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