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- PDB-8jwl: The first purified state crystal structure of AKRtyl -

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Basic information

Entry
Database: PDB / ID: 8jwl
TitleThe first purified state crystal structure of AKRtyl
ComponentsAldo/keto reductase
KeywordsOXIDOREDUCTASE / Aldo-keto reductase
Function / homologyNADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / cytosol / Chem-NDP / Aldo/keto reductase
Function and homology information
Biological speciesStreptomyces xinghaiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLin, S. / Dai, S. / Xiao, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21632007 China
CitationJournal: Nat Commun / Year: 2024
Title: A three-level regulatory mechanism of the aldo-keto reductase subfamily AKR12D.
Authors: Xiao, Z. / Zha, J. / Yang, X. / Huang, T. / Huang, S. / Liu, Q. / Wang, X. / Zhong, J. / Zheng, J. / Liang, R. / Deng, Z. / Zhang, J. / Lin, S. / Dai, S.
History
DepositionJun 29, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 10, 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: Aldo/keto reductase
B: Aldo/keto reductase
C: Aldo/keto reductase
D: Aldo/keto reductase
E: Aldo/keto reductase
F: Aldo/keto reductase
G: Aldo/keto reductase
H: Aldo/keto reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)309,21110
Polymers307,7218
Non-polymers1,4912
Water17,709983
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32130 Å2
ΔGint-98 kcal/mol
Surface area88710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.973, 183.092, 102.336
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab

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Components

#1: Protein
Aldo/keto reductase


Mass: 38465.078 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces xinghaiensis (bacteria) / Gene: DC095_024450, SFRA_012675 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3R7J519
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 983 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.56 Å3/Da / Density % sol: 51.9 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 22% PEG 400, 0.1M MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 31, 2020
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 139793 / % possible obs: 99.7 % / Redundancy: 10.9 % / Biso Wilson estimate: 27.33 Å2 / CC1/2: 0.982 / Rmerge(I) obs: 0.131 / Net I/σ(I): 16.8
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 1.064 / Num. unique obs: 6907 / CC1/2: 0.933

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-30007.21data scaling
PDB_EXTRACT4.1data extraction
HKL-30007.21data reduction
PHENIX1.17.1_3660phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→38.17 Å / SU ML: 0.2432 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.0284
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2312 6772 4.85 %RANDOM
Rwork0.1869 132752 --
obs0.1891 139524 99.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.39 Å2
Refinement stepCycle: LAST / Resolution: 2.3→38.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20068 0 0 983 21051
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011420511
X-RAY DIFFRACTIONf_angle_d1.076227861
X-RAY DIFFRACTIONf_chiral_restr0.05743002
X-RAY DIFFRACTIONf_plane_restr0.00553673
X-RAY DIFFRACTIONf_dihedral_angle_d30.6387440
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.330.31852120.2674284X-RAY DIFFRACTION97.15
2.33-2.350.2552510.20164337X-RAY DIFFRACTION99.96
2.35-2.380.27332270.20464453X-RAY DIFFRACTION99.98
2.38-2.410.24912350.19694337X-RAY DIFFRACTION99.98
2.41-2.450.26992290.1954394X-RAY DIFFRACTION99.94
2.45-2.480.262400.19954377X-RAY DIFFRACTION100
2.48-2.510.26712320.19724404X-RAY DIFFRACTION99.94
2.51-2.550.26912160.18834438X-RAY DIFFRACTION100
2.55-2.590.26122300.18874365X-RAY DIFFRACTION99.91
2.59-2.630.2562210.18954412X-RAY DIFFRACTION99.98
2.63-2.680.2712120.18734418X-RAY DIFFRACTION99.98
2.68-2.730.22482580.19014382X-RAY DIFFRACTION99.98
2.73-2.780.2312150.18064416X-RAY DIFFRACTION99.98
2.78-2.840.23582380.18774417X-RAY DIFFRACTION100
2.84-2.90.25652420.18364400X-RAY DIFFRACTION100
2.9-2.970.24522120.18824408X-RAY DIFFRACTION100
2.97-3.040.22662470.18524428X-RAY DIFFRACTION99.98
3.04-3.120.23962100.19294469X-RAY DIFFRACTION99.98
3.12-3.210.25392080.19694434X-RAY DIFFRACTION100
3.21-3.320.2731960.22524469X-RAY DIFFRACTION99.96
3.32-3.440.24022070.22624455X-RAY DIFFRACTION99.91
3.44-3.570.23012510.21134436X-RAY DIFFRACTION99.94
3.57-3.740.36012270.30434134X-RAY DIFFRACTION93.54
3.74-3.930.20841990.17514474X-RAY DIFFRACTION99.34
3.93-4.180.18262170.15274420X-RAY DIFFRACTION98.81
4.18-4.50.17082160.13694483X-RAY DIFFRACTION99.96
4.5-4.950.16052380.12984502X-RAY DIFFRACTION99.94
4.95-5.670.16972320.14034527X-RAY DIFFRACTION100
5.67-7.130.18052240.16284567X-RAY DIFFRACTION100
7.13-38.170.18872300.15594712X-RAY DIFFRACTION98.7

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