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- PDB-8wjw: Aldo-keto reductase KmAKR-W297H/Y296W -

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Basic information

Entry
Database: PDB / ID: 8wjw
TitleAldo-keto reductase KmAKR-W297H/Y296W
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: 1.5 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/Y296W from Kluyveromyces marxianus
Authors: Xu, S.Y. / Zhou, L. / Xu, Y. / Wang, Y.J. / Zheng, Y.G.
History
DepositionSep 26, 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


Theoretical massNumber of molelcules
Total (without water)35,4041
Polymers35,4041
Non-polymers00
Water5,531307
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.561, 64.796, 99.793
Angle α, β, γ (deg.)90.00, 105.54, 90.00
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-510-

HOH

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Components

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


Mass: 35404.176 Da / Num. of mol.: 1 / Mutation: 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.: 307 / 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: 2.36 Å3/Da / Density % sol: 47.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Sodium acetate trihydrate,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: 1.5→53.73 Å / Num. obs: 52646 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.04 / Rrim(I) all: 0.103 / Net I/σ(I): 11.6
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2 / Num. unique obs: 2632 / CC1/2: 0.881 / Rpim(I) all: 0.16 / Rrim(I) all: 0.387 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
DIALSdata scaling
DIALSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 1.5→53.73 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.195 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1809 2587 4.9 %RANDOM
Rwork0.15259 ---
obs0.15396 50056 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.97 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20.22 Å2
2---0.11 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.5→53.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2478 0 0 307 2785
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122533
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162433
X-RAY DIFFRACTIONr_angle_refined_deg1.141.6493435
X-RAY DIFFRACTIONr_angle_other_deg0.3941.5725645
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.25306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.75754
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.35210464
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0650.2389
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022838
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02530
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_it1.6481.471227
X-RAY DIFFRACTIONr_mcbond_other1.6211.4691227
X-RAY DIFFRACTIONr_mcangle_it2.3912.6361532
X-RAY DIFFRACTIONr_mcangle_other2.3912.6361533
X-RAY DIFFRACTIONr_scbond_it3.5041.8611306
X-RAY DIFFRACTIONr_scbond_other3.5021.8611307
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4693.2221904
X-RAY DIFFRACTIONr_long_range_B_refined6.27216.392998
X-RAY DIFFRACTIONr_long_range_B_other6.10715.442918
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.224 186 -
Rwork0.216 3668 -
obs--99.97 %

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