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- PDB-8iku: Aldo-keto reductase KmAKR - W297H -

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Basic information

Entry
Database: PDB / ID: 8iku
TitleAldo-keto reductase KmAKR - 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, NAD(P) as acceptor / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP 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: 2.13 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 - W297H from Kluyveromyces marxianus
Authors: Xu, S.Y. / Zhou, L. / Xu, Y. / Wang, Y.J. / Zheng, Y.G.
History
DepositionMar 1, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 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


Theoretical massNumber of molelcules
Total (without water)35,3811
Polymers35,3811
Non-polymers00
Water48627
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13560 Å2
Unit cell
Length a, b, c (Å)97.453, 48.031, 66.468
Angle α, β, γ (deg.)90.00, 104.01, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 35381.137 Da / Num. of mol.: 1 / Mutation: 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 / Water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.13 Å3/Da / Density % sol: 42.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Sodium acetate trihydrate,TRIS hydrochloride,PEG 4000,glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9792 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: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.13→64.49 Å / Num. obs: 16912 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.044 / Rrim(I) all: 0.114 / Net I/σ(I): 11.3
Reflection shellResolution: 2.13→2.17 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 2 / Num. unique obs: 867 / CC1/2: 0.897 / Rpim(I) all: 0.145 / Rrim(I) all: 0.373 / % possible all: 100

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Processing

Software
NameVersionClassification
DIALSdata scaling
REFMAC5refinement
DIALSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 2.13→64.49 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.921 / SU B: 9.192 / SU ML: 0.222 / Cross valid method: THROUGHOUT / ESU R: 0.297 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25973 878 5.2 %RANDOM
Rwork0.2125 ---
obs0.21498 16033 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.104 Å2
Baniso -1Baniso -2Baniso -3
1--0.95 Å2-0 Å20.19 Å2
2--3.42 Å20 Å2
3----2.27 Å2
Refinement stepCycle: 1 / Resolution: 2.13→64.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2476 0 0 27 2503
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122530
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162431
X-RAY DIFFRACTIONr_angle_refined_deg1.3371.6513430
X-RAY DIFFRACTIONr_angle_other_deg0.4221.5725641
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3975306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.84554
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.10810464
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0630.2389
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022836
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02528
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_it2.7193.5941227
X-RAY DIFFRACTIONr_mcbond_other2.7163.5941227
X-RAY DIFFRACTIONr_mcangle_it3.9476.4711532
X-RAY DIFFRACTIONr_mcangle_other3.9466.471533
X-RAY DIFFRACTIONr_scbond_it3.2463.8921303
X-RAY DIFFRACTIONr_scbond_other3.2453.8921304
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0736.9971899
X-RAY DIFFRACTIONr_long_range_B_refined6.24648.415526
X-RAY DIFFRACTIONr_long_range_B_other6.24448.415525
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.13→2.185 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 72 -
Rwork0.303 1186 -
obs--100 %

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