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- PDB-8wk5: Aldo-keto reductase KmAKR-Y28A/K29H/Y296W/W297H -

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Basic information

Entry
Database: PDB / ID: 8wk5
TitleAldo-keto reductase KmAKR-Y28A/K29H/Y296W/W297H
ComponentsNADPH-dependent alpha-keto amide reductase
KeywordsOXIDOREDUCTASE / apo-form / NADPH-dependent / beta-8/alpha-8-barrel
Function / homology
Function and homology information


oxidoreductase activity, acting on NAD(P)H as acceptor / :
Similarity search - Function
Aldo-keto reductase family 3C2/3 / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily
Similarity search - Domain/homology
NADPH-dependent alpha-keto amide reductase
Similarity search - Component
Biological speciesKluyveromyces marxianus (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsXu, S.Y. / Zhou, L. / Xu, Y. / Wang, Y.J. / Zheng, Y.G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22178318 China
CitationJournal: To Be Published
Title: Aldo-keto reductase KmAKR-Y28A/K29H/Y296W/W297H from Kluyveromyces marxianus
Authors: Xu, S.Y. / Zhou, L. / Xu, Y. / Wang, Y.J. / Zheng, Y.G.
History
DepositionSep 27, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NADPH-dependent alpha-keto amide reductase
B: NADPH-dependent alpha-keto amide reductase
C: NADPH-dependent alpha-keto amide reductase
D: NADPH-dependent alpha-keto amide reductase


Theoretical massNumber of molelcules
Total (without water)141,2844
Polymers141,2844
Non-polymers00
Water27015
1
A: NADPH-dependent alpha-keto amide reductase


Theoretical massNumber of molelcules
Total (without water)35,3211
Polymers35,3211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NADPH-dependent alpha-keto amide reductase


Theoretical massNumber of molelcules
Total (without water)35,3211
Polymers35,3211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: NADPH-dependent alpha-keto amide reductase


Theoretical massNumber of molelcules
Total (without water)35,3211
Polymers35,3211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: NADPH-dependent alpha-keto amide reductase


Theoretical massNumber of molelcules
Total (without water)35,3211
Polymers35,3211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.616, 115.979, 83.828
Angle α, β, γ (deg.)90.00, 102.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
NADPH-dependent alpha-keto amide reductase


Mass: 35321.047 Da / Num. of mol.: 4 / Mutation: Y28A,K29H,Y296W,W297H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces marxianus (yeast) / Gene: KLMA_60481 / Production host: Escherichia coli (E. coli) / References: UniProt: W0TDP7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.28 Å3/Da / Density % sol: 46.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Magnesium chloride hexahydrate, TRIS hydrochloride, Polyethylene glycol 4000, glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.9→115.98 Å / Num. obs: 27573 / % possible obs: 98.3 % / Redundancy: 2.9 % / CC1/2: 0.746 / Rmerge(I) obs: 0.437 / Rpim(I) all: 0.307 / Rrim(I) all: 0.536 / Χ2: 0.8 / Net I/σ(I): 3.8 / Num. measured all: 79136
Reflection shellResolution: 2.9→3.08 Å / % possible obs: 99.2 % / Redundancy: 2.8 % / Rmerge(I) obs: 1.988 / Num. measured all: 12375 / Num. unique obs: 4474 / CC1/2: 0.159 / Rpim(I) all: 1.439 / Rrim(I) all: 2.466 / Χ2: 0.69 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 2.9→57.86 Å / Cor.coef. Fo:Fc: 0.836 / Cor.coef. Fo:Fc free: 0.772 / SU B: 37.235 / SU ML: 0.637 / Cross valid method: THROUGHOUT / ESU R Free: 0.563 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31194 1343 4.9 %RANDOM
Rwork0.26763 ---
obs0.26983 26203 98.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.437 Å2
Baniso -1Baniso -2Baniso -3
1-5.42 Å20 Å24.1 Å2
2---3.07 Å2-0 Å2
3----3.79 Å2
Refinement stepCycle: 1 / Resolution: 2.9→57.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9672 0 0 15 9687
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0129881
X-RAY DIFFRACTIONr_bond_other_d0.0010.0169532
X-RAY DIFFRACTIONr_angle_refined_deg0.9241.65813392
X-RAY DIFFRACTIONr_angle_other_deg0.3011.57822106
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.36751192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.388516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.407101808
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0430.21524
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211130
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022062
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_it1.633.4014795
X-RAY DIFFRACTIONr_mcbond_other1.633.4014795
X-RAY DIFFRACTIONr_mcangle_it2.8716.1215978
X-RAY DIFFRACTIONr_mcangle_other2.876.1215979
X-RAY DIFFRACTIONr_scbond_it1.6243.5385086
X-RAY DIFFRACTIONr_scbond_other1.6243.5385087
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9636.4377415
X-RAY DIFFRACTIONr_long_range_B_refined5.3744.5420960
X-RAY DIFFRACTIONr_long_range_B_other5.3744.5420961
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 114 -
Rwork0.388 1919 -
obs--99.17 %

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