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- PDB-2fr0: The first ketoreductase of the erythromycin synthase (crystal form 1) -

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Basic information

Entry
Database: PDB / ID: 2fr0
TitleThe first ketoreductase of the erythromycin synthase (crystal form 1)
ComponentsErythromycin synthase, EryAI
KeywordsOXIDOREDUCTASE / Short Chain Dehydrogenase/Reductase
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
Similarity search - Function
PKS_PP_betabranch / Polyketide synthase, ketoreductase domain / KR domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Malonyl-CoA ACP transacylase, ACP-binding / PKS_KR / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain ...PKS_PP_betabranch / Polyketide synthase, ketoreductase domain / KR domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / 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 / 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 / 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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / 6-deoxyerythronolide-B synthase EryA1, modules 1 and 2
Similarity search - Component
Biological speciesSaccharopolyspora erythraea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.81 Å
AuthorsKeatinge-Clay, A.T. / Stroud, R.M.
CitationJournal: Structure / Year: 2006
Title: The Structure of a Ketoreductase Determines the Organization of the beta-Carbon Processing Enzymes of Modular Polyketide Synthases
Authors: Keatinge-Clay, A.T. / Stroud, R.M.
History
DepositionJan 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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 1.4Apr 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 synthase, EryAI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8242
Polymers51,0781
Non-polymers7451
Water3,243180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.211, 46.332, 61.506
Angle α, β, γ (deg.)94.73, 90.17, 98.89
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Erythromycin synthase, EryAI


Mass: 51078.121 Da / Num. of mol.: 1 / Fragment: residues 1444-1925
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharopolyspora erythraea (bacteria) / Gene: eryAI / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q03131, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.37 Å3/Da / Density % sol: 48.15 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.5 mg/mL protein, 5.05 mM HEPES, 75 mM NaCl, 0.5 mM DTT, 17.5% PEG3350, 0.1 M guanidinium hydrochloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 28, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 1.81→45.6 Å / Num. all: 40140 / Num. obs: 40140 / % possible obs: 93.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 1.8 % / Rsym value: 0.058 / Net I/σ(I): 8.1
Reflection shellResolution: 1.81→1.89 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 2 / Num. unique all: 4345 / % possible all: 80.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: SAD
Starting model: Ab Initio

Resolution: 1.81→45.6 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.263 4014 -random
Rwork0.235 ---
all0.235 40140 --
obs0.235 40140 93.7 %-
Refinement stepCycle: LAST / Resolution: 1.81→45.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3468 0 48 180 3696
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3nadph.param

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