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- PDB-5b1y: Crystal structure of NADPH bound carbonyl reductase from Aeropyru... -

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Basic information

Entry
Database: PDB / ID: 5b1y
TitleCrystal structure of NADPH bound carbonyl reductase from Aeropyrum pernix
Components3-oxoacyl-[acyl-carrier-protein] reductase
KeywordsOXIDOREDUCTASE / NAD(P)H-dependent carbonyl reductase / Aeropyrum pernix K1 / hyperthermophile / archaea
Function / homology
Function and homology information


3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / 3-oxoacyl-[acyl-carrier-protein] reductase / nucleotide binding
Similarity search - Function
PKS_KR / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / 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 / 3-oxoacyl-[acyl-carrier-protein] reductase
Similarity search - Component
Biological speciesAeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsYoneda, K. / Sakuraba, H. / Fukuda, Y. / Araki, T. / Ohshima, T.
CitationJournal: Enzyme.Microb.Technol. / Year: 2016
Title: Catalytic properties and crystal structure of thermostable NAD(P)H-dependent carbonyl reductase from the hyperthermophilic archaeon Aeropyrum pernix K1.
Authors: Fukuda, Y. / Sakuraba, H. / Araki, T. / Ohshima, T. / Yoneda, K.
History
DepositionDec 22, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Derived calculations
Category: diffrn_detector / diffrn_source / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: 3-oxoacyl-[acyl-carrier-protein] reductase
B: 3-oxoacyl-[acyl-carrier-protein] reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6534
Polymers58,1632
Non-polymers1,4912
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5700 Å2
ΔGint-29 kcal/mol
Surface area18800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.628, 91.628, 177.587
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 3-oxoacyl-[acyl-carrier-protein] reductase


Mass: 29081.311 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1) (archaea)
Strain: ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1
Gene: fabG, APE_2503.1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) codon plus RIPL
References: UniProt: Q9Y8Y1, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 3.47 Å3/Da / Density % sol: 64.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2.0 M NaCl, 0.1 M acetate buffer / PH range: 4.5-4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 45349 / % possible obs: 99.7 % / Redundancy: 15.9 % / Biso Wilson estimate: 22.9 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 10

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Processing

Software
NameVersionClassification
HKL-2000data processing
HKL-2000data scaling
MOLREPphasing
Cootmodel building
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2UVD

2uvd


Resolution: 2.09→33.1 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.2423 -5 %Random
Rwork0.2297 ---
obs-45264 99.7 %-
Displacement parametersBiso mean: 37.3 Å2
Refinement stepCycle: LAST / Resolution: 2.09→33.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3593 0 96 244 3933

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