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- PDB-6ket: Flavin-utilizing Monooxygenase (OX) Domain of Hybrid Polyketide/N... -

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Basic information

Entry
Database: PDB / ID: 6ket
TitleFlavin-utilizing Monooxygenase (OX) Domain of Hybrid Polyketide/Non-Ribosomal Peptide Synthetase
ComponentsPuwE
KeywordsOXIDOREDUCTASE / Monooxygenase / Hybrid Polyketide/Non-Ribosomal Peptide Synthetase
Function / homology
Function and homology information


fatty acid synthase activity / transaminase activity / phosphopantetheine binding / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / fatty acid biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
Natural product biosynthesis luciferase-like monooxygenase domain / Luciferase-like domain / Luciferase-like monooxygenase / Luciferase-like domain superfamily / CurL-like, PKS C-terminal / Condensation domain / Condensation domain / Amino acid adenylation domain / PKS_PP_betabranch / : ...Natural product biosynthesis luciferase-like monooxygenase domain / Luciferase-like domain / Luciferase-like monooxygenase / Luciferase-like domain superfamily / CurL-like, PKS C-terminal / Condensation domain / Condensation domain / Amino acid adenylation domain / PKS_PP_betabranch / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / 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 / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Chloramphenicol acetyltransferase-like domain superfamily / Putative AMP-binding domain signature. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / AMP-dependent synthetase/ligase / AMP-binding enzyme / 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 / AMP-binding enzyme, C-terminal domain superfamily / Thiolase-like / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Biological speciesCylindrospermum alatosporum CCALA 988 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsTian, Q.W. / Jiang, T.
CitationJournal: To Be Published
Title: Structure Insights into the Molecular Mechanism of Two Tailoring Domains of Hybrid Polyketide/Non-Ribosomal Peptide Synthetase
Authors: Tian, Q.W. / Jiang, T.
History
DepositionJul 5, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PuwE
B: PuwE


Theoretical massNumber of molelcules
Total (without water)80,2382
Polymers80,2382
Non-polymers00
Water7,692427
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-28 kcal/mol
Surface area25620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.610, 103.554, 77.225
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-406-

HOH

21A-659-

HOH

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Components

#1: Protein PuwE / flavin-utilizing monooxygenase


Mass: 40119.012 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cylindrospermum alatosporum CCALA 988 (bacteria)
Gene: puwE / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A0WDC6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 427 / 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: 2.38 Å3/Da / Density % sol: 48.37 %
Crystal growTemperature: 312 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M HEPES, pH 8.5, 0.2 M MgCl2, 20% (v/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.6→23.29 Å / Num. obs: 101260 / % possible obs: 99.52 % / Redundancy: 6.9 % / Biso Wilson estimate: 19.39 Å2 / Rpim(I) all: 0.045 / Rrim(I) all: 0.161 / Χ2: 3.238 / Net I/σ(I): 32.4
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 13.6 % / Mean I/σ(I) obs: 3.86 / Num. unique obs: 5285 / CC1/2: 0.943 / Rpim(I) all: 0.143 / Rrim(I) all: 0.528 / Χ2: 0.519 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.13-2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→23.29 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2388 2006 -
Rwork0.2204 --
obs0.2207 101204 99.58 %
Refinement stepCycle: LAST / Resolution: 1.6→23.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5307 0 0 427 5734
LS refinement shellResolution: 1.569→1.625 Å
RfactorNum. reflection% reflection
Rfree0.2723 --
Rwork0.2375 --
obs-10513 98.77 %

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