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- PDB-8jwo: Crystal structure of AKRtyl-tylosin complex -

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Basic information

Entry
Database: PDB / ID: 8jwo
TitleCrystal structure of AKRtyl-tylosin complex
ComponentsAldo/keto reductase
KeywordsOXIDOREDUCTASE / complex
Function / homologyNADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / cytosol / TYLOSIN / Aldo/keto reductase
Function and homology information
Biological speciesStreptomyces xinghaiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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
I: Aldo/keto reductase
J: Aldo/keto reductase
K: Aldo/keto reductase
L: Aldo/keto reductase
M: Aldo/keto reductase
N: Aldo/keto reductase
O: Aldo/keto reductase
P: Aldo/keto reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)630,09932
Polymers615,44116
Non-polymers14,65816
Water38,6782147
1
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)315,04916
Polymers307,7218
Non-polymers7,3298
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36030 Å2
ΔGint-107 kcal/mol
Surface area88310 Å2
MethodPISA
2
I: Aldo/keto reductase
J: Aldo/keto reductase
K: Aldo/keto reductase
L: Aldo/keto reductase
M: Aldo/keto reductase
N: Aldo/keto reductase
O: Aldo/keto reductase
P: Aldo/keto reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)315,04916
Polymers307,7218
Non-polymers7,3298
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36660 Å2
ΔGint-100 kcal/mol
Surface area88880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.021, 111.021, 560.041
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Space group name HallP4cw
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: -x,-y,z+1/2

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Components

#1: Protein
Aldo/keto reductase


Mass: 38465.078 Da / Num. of mol.: 16
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-TYK / TYLOSIN


Mass: 916.100 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C46H77NO17 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2147 / 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: 2.8 Å3/Da / Density % sol: 61.51 %
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: May 27, 2021
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 317806 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 27.64 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.13 / Net I/σ(I): 11.3
Reflection shellResolution: 2.25→2.29 Å / Rmerge(I) obs: 0.816 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 15864 / CC1/2: 0.699

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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: 2.25→49.74 Å / SU ML: 0.2413 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 21.7674
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2165 15524 4.93 %RANDOM
Rwork0.181 299061 --
obs0.1828 314585 99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.37 Å2
Refinement stepCycle: LAST / Resolution: 2.25→49.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms39036 0 0 2147 41183
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011639895
X-RAY DIFFRACTIONf_angle_d1.582454236
X-RAY DIFFRACTIONf_chiral_restr0.28736063
X-RAY DIFFRACTIONf_plane_restr0.01066993
X-RAY DIFFRACTIONf_dihedral_angle_d30.664814167
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.280.27874480.24219322X-RAY DIFFRACTION91.44
2.28-2.30.26964930.23839464X-RAY DIFFRACTION94.43
2.3-2.330.28125100.23769650X-RAY DIFFRACTION96.74
2.33-2.360.27124980.23299986X-RAY DIFFRACTION98.05
2.36-2.390.28284730.23069874X-RAY DIFFRACTION98.62
2.39-2.430.27565140.22179981X-RAY DIFFRACTION99.09
2.43-2.460.26045590.228910088X-RAY DIFFRACTION99.71
2.46-2.50.26125350.22069927X-RAY DIFFRACTION99.73
2.5-2.540.22865090.201210109X-RAY DIFFRACTION99.99
2.54-2.580.23535440.197610050X-RAY DIFFRACTION99.97
2.58-2.620.23775510.192810004X-RAY DIFFRACTION99.99
2.62-2.670.23854750.18610106X-RAY DIFFRACTION99.97
2.67-2.720.23755370.186910050X-RAY DIFFRACTION100
2.72-2.780.25144890.18310101X-RAY DIFFRACTION99.97
2.78-2.840.23695070.183510051X-RAY DIFFRACTION99.99
2.84-2.90.22815440.17210046X-RAY DIFFRACTION100
2.9-2.970.22824510.174310149X-RAY DIFFRACTION99.98
2.97-3.060.22655060.180910043X-RAY DIFFRACTION99.9
3.06-3.150.20715080.170510093X-RAY DIFFRACTION99.94
3.15-3.250.22515060.170310056X-RAY DIFFRACTION99.99
3.25-3.360.21855240.174910125X-RAY DIFFRACTION99.99
3.36-3.50.20595560.169810019X-RAY DIFFRACTION100
3.5-3.660.19355280.160210045X-RAY DIFFRACTION100
3.66-3.850.18475240.159710072X-RAY DIFFRACTION100
3.85-4.090.18715540.153410010X-RAY DIFFRACTION99.94
4.09-4.410.17735320.149410056X-RAY DIFFRACTION99.98
4.41-4.850.17575520.155910042X-RAY DIFFRACTION99.91
4.85-5.550.19185220.175110119X-RAY DIFFRACTION99.95
5.55-6.990.2315530.202510013X-RAY DIFFRACTION99.88
6.99-49.740.20835220.19289410X-RAY DIFFRACTION93.13

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