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- PDB-8y7r: Crystal structure of a novel ketoreductase from Sphingobacterium ... -

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Basic information

Entry
Database: PDB / ID: 8y7r
TitleCrystal structure of a novel ketoreductase from Sphingobacterium siyangense SY1
ComponentsNAD(P)-dependent dehydrogenase (Short-subunit alcohol dehydrogenase family)
KeywordsOXIDOREDUCTASE / SSDR / catalysis / reaction
Function / homology
Function and homology information


monocarboxylic acid metabolic process / lipid metabolic process / nucleotide binding
Similarity search - Function
: / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NAD(P)-dependent dehydrogenase (Short-subunit alcohol dehydrogenase family)
Similarity search - Component
Biological speciesSphingobacterium siyangense (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsZheng, Z.R. / Wei, H.L. / Liu, W.D. / You, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Structure-based reshaping of a new ketoreductase from Sphingobacterium siyangense SY1 toward alpha-haloacetophenones.
Authors: Che, C. / Zhang, W. / Xu, X. / Zheng, Z. / Wei, H. / Qin, B. / Jia, X. / Liu, W. / You, S.
History
DepositionFeb 5, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NAD(P)-dependent dehydrogenase (Short-subunit alcohol dehydrogenase family)
B: NAD(P)-dependent dehydrogenase (Short-subunit alcohol dehydrogenase family)


Theoretical massNumber of molelcules
Total (without water)51,8932
Polymers51,8932
Non-polymers00
Water5,314295
1
A: NAD(P)-dependent dehydrogenase (Short-subunit alcohol dehydrogenase family)
B: NAD(P)-dependent dehydrogenase (Short-subunit alcohol dehydrogenase family)

A: NAD(P)-dependent dehydrogenase (Short-subunit alcohol dehydrogenase family)
B: NAD(P)-dependent dehydrogenase (Short-subunit alcohol dehydrogenase family)


Theoretical massNumber of molelcules
Total (without water)103,7864
Polymers103,7864
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_544x,x-y-1,-z-1/61
Buried area12400 Å2
ΔGint-92 kcal/mol
Surface area33130 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-24 kcal/mol
Surface area20150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.580, 84.580, 280.980
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11B-323-

HOH

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Components

#1: Protein NAD(P)-dependent dehydrogenase (Short-subunit alcohol dehydrogenase family)


Mass: 25946.461 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingobacterium siyangense (bacteria) / Gene: IQ31_01205
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A562MSV3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 25%PEG 550, 0.02M MgCl2, 0.1M Bis-Tris pH7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17UM / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.62→57.77 Å / Num. obs: 76711 / % possible obs: 100 % / Redundancy: 42.1 % / CC1/2: 1 / Net I/σ(I): 32.5
Reflection shellResolution: 1.62→1.66 Å / Redundancy: 43.4 % / Num. unique obs: 5572 / CC1/2: 0.791 / Χ2: 0.93

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.62→57.77 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.416 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18943 3804 5 %RANDOM
Rwork0.16653 ---
obs0.16765 72765 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.762 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20.11 Å20 Å2
2--0.23 Å2-0 Å2
3----0.74 Å2
Refinement stepCycle: 1 / Resolution: 1.62→57.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3592 0 0 295 3887
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0123661
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163513
X-RAY DIFFRACTIONr_angle_refined_deg1.8061.794945
X-RAY DIFFRACTIONr_angle_other_deg0.641.7388095
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3385490
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.05458
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.17610605
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0970.2561
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024302
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02774
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8452.9681969
X-RAY DIFFRACTIONr_mcbond_other2.8442.9681969
X-RAY DIFFRACTIONr_mcangle_it3.9085.322456
X-RAY DIFFRACTIONr_mcangle_other3.9075.322457
X-RAY DIFFRACTIONr_scbond_it4.7893.481692
X-RAY DIFFRACTIONr_scbond_other4.7873.481693
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.1526.1572490
X-RAY DIFFRACTIONr_long_range_B_refined8.06130.964180
X-RAY DIFFRACTIONr_long_range_B_other8.01829.74100
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.62→1.662 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 259 -
Rwork0.248 5305 -
obs--99.95 %

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