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Basic information

Entry
Database: PDB / ID: 5ywn
TitleSsCR_L211H-NADP+
ComponentsProtein induced by osmotic stress
KeywordsOXIDOREDUCTASE / reductase / asymmetric reduction / substrate inhibition
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 / Resolution: 2.039 Å
AuthorsShang, Y.P. / Chen, Q. / 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 29, 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 1.2Mar 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: Protein induced by osmotic stress
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7742
Polymers37,0311
Non-polymers7431
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-3 kcal/mol
Surface area14540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.782, 53.093, 70.768
Angle α, β, γ (deg.)90.00, 95.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein induced by osmotic stress


Mass: 37030.855 Da / Num. of mol.: 1 / Mutation: L211H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Scheffersomyces stipitis (strain ATCC 58785 / CBS 6054 / NBRC 10063 / NRRL Y-11545) (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.: 228 / 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: 2.37 Å3/Da / Density % sol: 48.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2M lithium sulfate monohydrate, 0.1M Tris hydrochloride (pH 8.0), 33% (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: 2.039→35.221 Å / Num. obs: 21629 / % possible obs: 98.3 % / Redundancy: 4 % / Net I/σ(I): 11.4
Reflection shellResolution: 2.04→2.08 Å

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.039→35.221 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.223 1092 5.05 %
Rwork0.1657 --
obs0.1685 21609 97.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.039→35.221 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2609 0 48 228 2885
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072714
X-RAY DIFFRACTIONf_angle_d0.8243685
X-RAY DIFFRACTIONf_dihedral_angle_d15.7491627
X-RAY DIFFRACTIONf_chiral_restr0.051421
X-RAY DIFFRACTIONf_plane_restr0.005464
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0387-2.13150.21731200.16562400X-RAY DIFFRACTION91
2.1315-2.24390.26031330.16762601X-RAY DIFFRACTION100
2.2439-2.38440.26171340.17142637X-RAY DIFFRACTION100
2.3844-2.56850.251560.18062595X-RAY DIFFRACTION100
2.5685-2.82690.22471440.17422627X-RAY DIFFRACTION100
2.8269-3.23570.22931500.17022605X-RAY DIFFRACTION99
3.2357-4.07560.19321250.16072543X-RAY DIFFRACTION96
4.0756-35.22620.21191300.15582509X-RAY DIFFRACTION92

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