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- PDB-7emg: Carbonyl Reductase Variant 4 (R123C/L209P/F183Y/V61K) from Serrat... -

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Basic information

Entry
Database: PDB / ID: 7emg
TitleCarbonyl Reductase Variant 4 (R123C/L209P/F183Y/V61K) from Serratia marcescens complexed with NADP+
Components3-oxoacyl-[acyl-carrier-protein] reductase
KeywordsOXIDOREDUCTASE / NADP+ complex / carbonyl reductase
Function / homology
Function and homology information


: / : / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / NAD binding / fatty acid biosynthetic process
Similarity search - Function
3-oxoacyl-(acyl-carrier-protein) reductase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Chem-NDP / 3-oxoacyl-[acyl-carrier-protein] reductase
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.449 Å
AuthorsZheng, Y.C. / Wang, T. / Bai, Y.P.
CitationJournal: Chem.Commun.(Camb.) / Year: 2021
Title: Stereoselective synthesis of chiral delta-lactones via an engineered carbonyl reductase.
Authors: Wang, T. / Zhang, X.Y. / Zheng, Y.C. / Bai, Y.P.
History
DepositionApr 14, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)54,8025
Polymers53,2492
Non-polymers1,5533
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-15 kcal/mol
Surface area19110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.841, 120.299, 120.664
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein 3-oxoacyl-[acyl-carrier-protein] reductase


Mass: 26624.428 Da / Num. of mol.: 2 / Mutation: V61K, R123C, F183Y, L209P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria)
Gene: fabG, A8A12_06940, AR325_11665, BVG93_06205, G3M86_05635, G3M87_05635, G3M88_05635, G3M89_05635, GV243_09700, HMI62_09690
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0G8B235, 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: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.18 Å3/Da / Density % sol: 43.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M Sodium formate; 0.1M Ammonium acetate; 0.1M Sodium citrate tribasic dihydrate; 0.1M Potassium sodium tartrate tetrahydrate; 0.1M Sodium oxamate; 0.1M Imidazole; 0.1M MES monohydrate ...Details: 0.1M Sodium formate; 0.1M Ammonium acetate; 0.1M Sodium citrate tribasic dihydrate; 0.1M Potassium sodium tartrate tetrahydrate; 0.1M Sodium oxamate; 0.1M Imidazole; 0.1M MES monohydrate (acid); pH 6.5; 12.5% v/v MPD; 12.5% PEG 1000; 12.5% w/v PEG 3350
PH range: 6.5-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.449→50 Å / Num. obs: 17156 / % possible obs: 99 % / Redundancy: 12.8 % / Biso Wilson estimate: 33.5 Å2 / CC1/2: 0.969 / CC star: 0.992 / Χ2: 0.878 / Net I/σ(I): 15
Reflection shellResolution: 2.449→2.49 Å / Mean I/σ(I) obs: 4.1 / Num. unique obs: 849 / CC1/2: 0.954 / CC star: 0.988 / Χ2: 1.016

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1q7c

1q7c


Resolution: 2.449→42.596 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2588 661 4.59 %
Rwork0.1999 13755 -
obs0.2027 14416 82.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.79 Å2 / Biso mean: 35.7916 Å2 / Biso min: 15.51 Å2
Refinement stepCycle: final / Resolution: 2.449→42.596 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3480 0 83 58 3621
Biso mean--57.58 30.6 -
Num. residues----476
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023603
X-RAY DIFFRACTIONf_angle_d0.4894866
X-RAY DIFFRACTIONf_chiral_restr0.042569
X-RAY DIFFRACTIONf_plane_restr0.002617
X-RAY DIFFRACTIONf_dihedral_angle_d7.8112127
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.449-2.63780.3274750.2387189557
2.6378-2.90320.31881040.2379227069
2.9032-3.32310.27231460.2156288988
3.3231-4.18620.24941830.1855325498
4.1862-42.5960.23571530.1883344799

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