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- PDB-8jwm: Crystal structure of AKRtyl-NADP-tylosin complex -

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Basic information

Entry
Database: PDB / ID: 8jwm
TitleCrystal structure of AKRtyl-NADP-tylosin complex
ComponentsAldo/keto reductase
KeywordsOXIDOREDUCTASE / complex
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding / cytosol
Similarity search - Function
: / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / TYLOSIN / Aldo/keto reductase
Similarity search - Component
Biological speciesStreptomyces xinghaiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 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)320,08123
Polymers307,7218
Non-polymers12,36015
Water45,0922503
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area47060 Å2
ΔGint-129 kcal/mol
Surface area86770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.007, 198.310, 199.987
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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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-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-TYK / TYLOSIN


Mass: 916.100 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C46H77NO17 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2503 / 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: 2.83 Å3/Da / Density % sol: 56.61 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 18% PEG 3350, 0.1 M Sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 5, 2021
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. obs: 245855 / % possible obs: 99.9 % / Redundancy: 6.2 % / Biso Wilson estimate: 19.29 Å2 / CC1/2: 0.957 / Rmerge(I) obs: 0.133 / Net I/σ(I): 15.6
Reflection shellResolution: 1.93→1.96 Å / Rmerge(I) obs: 0.766 / Mean I/σ(I) obs: 2.33 / Num. unique obs: 12190 / CC1/2: 0.788

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-30007.21data scaling
PDB_EXTRACT4.1data extraction
HKL-30007.21data reduction
PHASER2.7.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→35.15 Å / SU ML: 0.171 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.755
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1979 11925 4.87 %RANDOM
Rwork0.1642 232960 --
obs0.1659 244885 98.68 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.91 Å2
Refinement stepCycle: LAST / Resolution: 1.93→35.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21276 0 0 2503 23779
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009121776
X-RAY DIFFRACTIONf_angle_d1.110629679
X-RAY DIFFRACTIONf_chiral_restr0.25393251
X-RAY DIFFRACTIONf_plane_restr0.00563826
X-RAY DIFFRACTIONf_dihedral_angle_d18.09597690
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.950.25633120.2245586X-RAY DIFFRACTION72.35
1.95-1.970.25663860.2147835X-RAY DIFFRACTION99.94
1.97-20.25523810.20587782X-RAY DIFFRACTION99.93
2-2.020.22953970.20377827X-RAY DIFFRACTION99.9
2.02-2.050.25383820.20987740X-RAY DIFFRACTION99.8
2.05-2.080.24443840.20117858X-RAY DIFFRACTION99.83
2.08-2.110.21964030.18957759X-RAY DIFFRACTION99.94
2.11-2.140.22224260.18837767X-RAY DIFFRACTION99.77
2.14-2.170.23364040.18157814X-RAY DIFFRACTION99.96
2.17-2.210.21954310.1797768X-RAY DIFFRACTION99.91
2.21-2.240.22974230.17447788X-RAY DIFFRACTION99.71
2.24-2.290.22444330.16897730X-RAY DIFFRACTION99.95
2.29-2.330.19553830.16757864X-RAY DIFFRACTION99.83
2.33-2.380.22274130.1727800X-RAY DIFFRACTION99.76
2.38-2.430.22094440.16987785X-RAY DIFFRACTION99.93
2.43-2.490.22394110.17647775X-RAY DIFFRACTION99.88
2.49-2.550.21984150.17477827X-RAY DIFFRACTION99.81
2.55-2.620.21464120.17017832X-RAY DIFFRACTION99.83
2.62-2.690.18724170.15947815X-RAY DIFFRACTION99.79
2.69-2.780.19613480.16717893X-RAY DIFFRACTION99.83
2.78-2.880.20363770.16897890X-RAY DIFFRACTION99.92
2.88-2.990.21363950.16747853X-RAY DIFFRACTION99.79
2.99-3.130.19814320.16727838X-RAY DIFFRACTION99.79
3.13-3.30.18994160.16087886X-RAY DIFFRACTION99.72
3.3-3.50.19013690.1587890X-RAY DIFFRACTION99.64
3.5-3.770.17033840.14727946X-RAY DIFFRACTION99.5
3.77-4.150.1613930.13177918X-RAY DIFFRACTION99.38
4.15-4.750.15173610.12837954X-RAY DIFFRACTION99.2
4.75-5.980.14483660.1438014X-RAY DIFFRACTION98.59
5.98-35.150.17994270.16477926X-RAY DIFFRACTION95.21

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