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- PDB-5yw4: Structure-Guided Engineering of Reductase: Efficient Attenuating ... -

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Basic information

Entry
Database: PDB / ID: 5yw4
TitleStructure-Guided Engineering of Reductase: Efficient Attenuating Substrate Inhibition in Asymmetric Catalysis
ComponentsProtein induced by osmotic stress
KeywordsOXIDOREDUCTASE / reductase / NADP+ / asymmetric catalysis
Function / homology
Function and homology information


cinnamyl-alcohol dehydrogenase / cinnamyl-alcohol dehydrogenase activity / nucleotide binding
Similarity search - Function
: / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Protein induced by osmotic stress
Similarity search - Component
Biological speciesScheffersomyces stipitis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.047 Å
AuthorsShang, Y.P. / Chen, Q. / Li, A.T. / Yu, H.L. / Xu, J.H.
CitationJournal: J.Biotechnol. / Year: 2020
Title: Attenuated substrate inhibition of a haloketone reductase via structure-guided loop engineering.
Authors: Shang, Y.P. / Chen, Q. / Li, A.T. / Quan, S. / Xu, J.H. / Yu, H.L.
History
DepositionNov 28, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 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: Protein induced by osmotic stress
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7492
Polymers37,0061
Non-polymers7431
Water3,351186
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-4 kcal/mol
Surface area14600 Å2
Unit cell
Length a, b, c (Å)47.035, 52.777, 70.996
Angle α, β, γ (deg.)90.00, 95.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein induced by osmotic stress


Mass: 37005.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Scheffersomyces stipitis (fungus) / Strain: ATCC 58785 / CBS 6054 / NBRC 10063 / NRRL Y-11545 / Gene: GRP3.1, PICST_32463
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A3LWG4, cinnamyl-alcohol dehydrogenase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.51 Å3/Da / Density % sol: 51.04 %
Description: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M lithium sulfate monohydrate, 0.1 M Tris hydrochloride (pH 8.0), 30% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.04→37.565 Å / Num. obs: 20904 / % possible obs: 95.3 % / Redundancy: 3 % / Net I/σ(I): 13.2
Reflection shellResolution: 2.04→2.09 Å

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GMO

5gmo


Resolution: 2.047→37.565 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.77 / Stereochemistry target values: ML
Details: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
RfactorNum. reflection% reflection
Rfree0.2584 1066 5.1 %
Rwork0.1935 --
obs0.1965 20904 94.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.047→37.565 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2591 0 48 186 2825
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082695
X-RAY DIFFRACTIONf_angle_d1.4033659
X-RAY DIFFRACTIONf_dihedral_angle_d15.484991
X-RAY DIFFRACTIONf_chiral_restr0.282419
X-RAY DIFFRACTIONf_plane_restr0.005460
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0472-2.14040.34121150.26862325X-RAY DIFFRACTION90
2.1404-2.25320.31141480.2442480X-RAY DIFFRACTION96
2.2532-2.39440.2851380.22312556X-RAY DIFFRACTION98
2.3944-2.57920.29931500.21012507X-RAY DIFFRACTION98
2.5792-2.83870.28521420.20752571X-RAY DIFFRACTION98
2.8387-3.24930.2731260.19612552X-RAY DIFFRACTION97
3.2493-4.09290.24911050.1732506X-RAY DIFFRACTION94
4.0929-37.5710.21141420.17332341X-RAY DIFFRACTION88

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