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- PDB-4l4x: An A2-type ketoreductase from a modular polyketide synthase -

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Basic information

Entry
Database: PDB / ID: 4l4x
TitleAn A2-type ketoreductase from a modular polyketide synthase
ComponentsAmphI
KeywordsOXIDOREDUCTASE / Rossmann fold / Ketoreductase
Function / homology
Function and homology information


phosphopantetheine binding / antibiotic biosynthetic process / transferase activity / nucleotide binding
Similarity search - Function
Polyketide synthase dimerisation element domain / Polyketide synthase dimerisation element domain / : / Polyketide synthase, docking domain / Erythronolide synthase docking domain / Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain ...Polyketide synthase dimerisation element domain / Polyketide synthase dimerisation element domain / : / Polyketide synthase, docking domain / Erythronolide synthase docking domain / 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 / Malonyl-CoA ACP transacylase, ACP-binding / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / 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. / 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
Biological speciesStreptomyces nodosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsZheng, J. / Keatinge-Clay, A.T.
CitationJournal: Acs Chem.Biol. / Year: 2013
Title: Structural Studies of an A2-Type Modular Polyketide Synthase Ketoreductase Reveal Features Controlling alpha-Substituent Stereochemistry.
Authors: Zheng, J. / Piasecki, S.K. / Keatinge-Clay, A.T.
History
DepositionJun 10, 2013Deposition site: RCSB / Processing site: RCSB
SupersessionJun 19, 2013ID: 4DI7
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Sep 20, 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AmphI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0732
Polymers61,3271
Non-polymers7451
Water1086
1
A: AmphI
hetero molecules

A: AmphI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,1454
Polymers122,6552
Non-polymers1,4912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3940 Å2
ΔGint-17 kcal/mol
Surface area43100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.139, 133.513, 185.137
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein AmphI


Mass: 61327.316 Da / Num. of mol.: 1
Fragment: Dimerization Element and Ketoreductase, UNP residues 4200-4759
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces nodosus (bacteria) / Gene: amphI / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q93NX9, 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.: 6 / 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: 2.27 Å3/Da / Density % sol: 45.91 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.213 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 28, 2011
RadiationMonochromator: Double-crystal, Si(111) liquid N2 cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.213 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. all: 18698 / Num. obs: 18174 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 %
Reflection shellResolution: 2.55→2.59 Å / Redundancy: 6 % / Rmerge(I) obs: 0.791 / Mean I/σ(I) obs: 2.2 / Num. unique all: 933 / Rsym value: 0.022 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHASESphasing
REFMAC5refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MJS

3mjs


Resolution: 2.55→50 Å / σ(F): 2.2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.28 909 -Random
Rwork0.227 ---
all0.23 18698 --
obs0.23 18174 97.3 %-
Refinement stepCycle: LAST / Resolution: 2.55→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3764 0 48 6 3818
LS refinement shellHighest resolution: 2.55 Å
RfactorNum. reflection% reflection
Rfree0.28 909 -
Rwork0.227 --
obs-18174 97.2 %

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