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

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Entry
Database: PDB / ID: 2fr0
TitleThe first ketoreductase of the erythromycin synthase (crystal form 1)
ComponentsErythromycin synthase, EryAI
KeywordsOXIDOREDUCTASE / Short Chain Dehydrogenase/Reductase
Function / homologyPolyketide synthase, acyl transferase domain / Beta-ketoacyl synthase, active site / Beta-ketoacyl synthase, C-terminal domain / Acyl transferase domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase, N-terminal domain / ACP-like superfamily / NAD(P)-binding domain superfamily / Ketoacyl-synthetase, C-terminal extension / Polyketide synthase, beta-ketoacyl synthase domain ...Polyketide synthase, acyl transferase domain / Beta-ketoacyl synthase, active site / Beta-ketoacyl synthase, C-terminal domain / Acyl transferase domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase, N-terminal domain / ACP-like superfamily / NAD(P)-binding domain superfamily / Ketoacyl-synthetase, C-terminal extension / Polyketide synthase, beta-ketoacyl synthase domain / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site. / Thiolase-like / Ketoacyl-synthetase C-terminal extension / Malonyl-CoA ACP transacylase, ACP-binding / Acyl transferase/acyl hydrolase/lysophospholipase / Acyl transferase / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal / Polyketide synthase, ketoreductase domain / Phosphopantetheine binding ACP domain / Phosphopantetheine attachment site / Acyl transferase domain superfamily / Beta-ketoacyl synthases active site. / Carrier protein (CP) domain profile. / KR domain / 6-deoxyerythronolide-B synthase / erythronolide synthase activity / macrolide biosynthetic process / phosphopantetheine binding / 6-deoxyerythronolide-B synthase EryA1, modules 1 and 2
Function and homology information
Specimen sourceSaccharopolyspora erythraea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / 1.81 Å resolution
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 18, 2006 / Release: Apr 4, 2006
RevisionDateData content typeGroupProviderType
1.0Apr 4, 2006Structure modelrepositoryInitial release
1.1May 1, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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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
Polyers51,0781
Non-polymers7451
Water3,243180
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
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-MP 1

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Components

#1: Protein/peptide Erythromycin synthase, EryAI


Mass: 51078.121 Da / Num. of mol.: 1 / Fragment: residues 1444-1925 / Source: (gene. exp.) Saccharopolyspora erythraea (bacteria) / Genus: Saccharopolyspora / Gene: eryAI / Plasmid name: pET28b / Genus (production host): Escherichia / 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


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


Mass: 18.015 Da / Num. of mol.: 180 / Formula: H2O / Water

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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 / Density percent sol: 48.15 %
Crystal growTemp: 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 kelvins
SourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Collection date: May 28, 2005
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionD resolution high: 1.81 Å / D resolution low: 45.6 Å / Number all: 40140 / Number obs: 40140 / Observed criterion sigma F: 1 / Observed criterion sigma I: 1 / Rsym value: 0.058 / NetI over sigmaI: 8.1 / Redundancy: 1.8 % / Percent possible obs: 93.7
Reflection shellRmerge I obs: 0.302 / Highest resolution: 1.81 Å / Lowest resolution: 1.89 Å / MeanI over sigI obs: 2 / Number unique all: 4345 / Redundancy: 1.6 % / Percent possible all: 80.9

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Processing

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

R Free selection details: random / Cross valid method: THROUGHOUT / Sigma F: 2 / Sigma I: 1 / Stereochemistry target values: Engh & Huber
Least-squares processR factor R free: 0.263 / R factor R work: 0.235 / R factor all: 0.235 / R factor obs: 0.235 / Highest resolution: 1.81 Å / Lowest resolution: 45.6 Å / Number reflection R free: 4014 / Number reflection all: 40140 / Number reflection obs: 40140 / Percent reflection obs: 93.7
Refine hist #LASTHighest resolution: 1.81 Å / Lowest resolution: 45.6 Å
Number of atoms included #LASTProtein: 3468 / Nucleic acid: 0 / Ligand: 48 / Solvent: 180 / Total: 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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