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- PDB-8y83: Crystal structure of a ketoreductase from Sphingobacterium siyang... -

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Basic information

Entry
Database: PDB / ID: 8y83
TitleCrystal structure of a ketoreductase from Sphingobacterium siyangense SY1 with co-enzyme
ComponentsNAD(P)-dependent dehydrogenase (Short-subunit alcohol dehydrogenase family)
KeywordsOXIDOREDUCTASE / SSDR / catalysis / reaction
Function / homology
Function and homology information


oxidoreductase activity / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD(P)-dependent dehydrogenase (Short-subunit alcohol dehydrogenase family)
Similarity search - Component
Biological speciesSphingobacterium siyangense (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 / _pdbx_entry_details.has_protein_modification

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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)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2204
Polymers51,8932
Non-polymers1,3272
Water2,414134
1
A: NAD(P)-dependent dehydrogenase (Short-subunit alcohol dehydrogenase family)
B: NAD(P)-dependent dehydrogenase (Short-subunit alcohol dehydrogenase family)
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)106,4408
Polymers103,7864
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_544x,x-y-1,-z-1/61
Buried area16980 Å2
ΔGint-112 kcal/mol
Surface area31780 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-35 kcal/mol
Surface area19480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.434, 84.434, 280.321
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-443-

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: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.73 Å3/Da / Density % sol: 55.01 %
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: BL10U2 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 38601 / % possible obs: 93.8 % / Redundancy: 62.4 % / CC1/2: 1 / Net I/σ(I): 28.63
Reflection shell
Resolution (Å)Num. unique obsCC1/2Diffraction-ID
2-2.1252270.8451
2.12-2.2751500.9541
2.27-2.4557230.9871
2.45-2.6852910.9961
2.68-2.9948290.9981
2.99-3.4641480.9991
3.46-4.2335110.9991
4.23-5.9529240.9991
5.95-50179811

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→44.53 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.337 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20057 1918 5 %RANDOM
Rwork0.16634 ---
obs0.16801 36683 93.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.636 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20.31 Å20 Å2
2--0.61 Å2-0 Å2
3----1.99 Å2
Refinement stepCycle: 1 / Resolution: 2→44.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3702 0 0 134 3836
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0123765
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163562
X-RAY DIFFRACTIONr_angle_refined_deg1.6481.7915101
X-RAY DIFFRACTIONr_angle_other_deg0.5791.7368214
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3875491
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.217510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.91710608
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0880.2582
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024359
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02791
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_it3.4753.951973
X-RAY DIFFRACTIONr_mcbond_other3.4753.951973
X-RAY DIFFRACTIONr_mcangle_it4.7777.0812461
X-RAY DIFFRACTIONr_mcangle_other4.7767.082462
X-RAY DIFFRACTIONr_scbond_it5.5284.5331792
X-RAY DIFFRACTIONr_scbond_other5.5264.5331793
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.1638.0832641
X-RAY DIFFRACTIONr_long_range_B_refined9.13139.344173
X-RAY DIFFRACTIONr_long_range_B_other9.12839.314153
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.051 Å
RfactorNum. reflection% reflection
Rfree0.262 158 -
Rwork0.227 2787 -
obs--99.49 %

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