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- PDB-8jwk: The second purified state crystal structure of AKRtyl -

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Basic information

Entry
Database: PDB / ID: 8jwk
TitleThe second purified state crystal structure of AKRtyl
ComponentsAldo/keto reductase
KeywordsOXIDOREDUCTASE / Aldo-keto reductase
Function / homology: / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / oxidoreductase activity / nucleotide binding / cytosol / Chem-NDP / Aldo/keto reductase
Function and homology information
Biological speciesStreptomyces xinghaiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 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

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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)620,03623
Polymers615,44116
Non-polymers4,5957
Water29,5091638
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)309,21110
Polymers307,7218
Non-polymers1,4912
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31950 Å2
ΔGint-110 kcal/mol
Surface area85980 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)310,82413
Polymers307,7218
Non-polymers3,1045
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34620 Å2
ΔGint-113 kcal/mol
Surface area85080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.894, 111.894, 563.243
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-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1638 / 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: 2.87 Å3/Da / Density % sol: 57.07 %
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: Nov 9, 2020
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.32→50 Å / Num. obs: 296368 / % possible obs: 100 % / Redundancy: 5.6 % / Biso Wilson estimate: 37.17 Å2 / CC1/2: 0.965 / Rmerge(I) obs: 0.16 / Net I/σ(I): 11.9
Reflection shellResolution: 2.32→2.36 Å / Rmerge(I) obs: 0.665 / Mean I/σ(I) obs: 2 / Num. unique obs: 14820 / CC1/2: 0.768

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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: 2.32→35.38 Å / SU ML: 0.2655 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 21.9902
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2172 14730 4.98 %RANDOM
Rwork0.1815 280936 --
obs0.1833 295666 99.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.89 Å2
Refinement stepCycle: LAST / Resolution: 2.32→35.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms38362 0 0 1638 40000
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017339176
X-RAY DIFFRACTIONf_angle_d1.421953193
X-RAY DIFFRACTIONf_chiral_restr0.07465787
X-RAY DIFFRACTIONf_plane_restr0.00936944
X-RAY DIFFRACTIONf_dihedral_angle_d31.115314184
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.340.27453640.22847886X-RAY DIFFRACTION82.79
2.34-2.370.27415120.22769361X-RAY DIFFRACTION100
2.37-2.40.26585050.22249422X-RAY DIFFRACTION100
2.4-2.430.26515080.21449507X-RAY DIFFRACTION100
2.43-2.460.23654600.21359326X-RAY DIFFRACTION100
2.46-2.50.284670.21319517X-RAY DIFFRACTION100
2.5-2.530.25255130.21249423X-RAY DIFFRACTION100
2.53-2.570.24294950.20149418X-RAY DIFFRACTION100
2.57-2.610.26374990.20699432X-RAY DIFFRACTION100
2.61-2.650.24454920.20019398X-RAY DIFFRACTION100
2.65-2.70.27284830.19469403X-RAY DIFFRACTION100
2.7-2.750.26145330.19949463X-RAY DIFFRACTION100
2.75-2.80.23374910.19049414X-RAY DIFFRACTION100
2.8-2.860.25765370.1999390X-RAY DIFFRACTION100
2.86-2.920.2444570.1939418X-RAY DIFFRACTION100
2.92-2.990.254560.19739484X-RAY DIFFRACTION99.99
2.99-3.060.24855190.19859387X-RAY DIFFRACTION100
3.06-3.140.23875080.19939413X-RAY DIFFRACTION100
3.14-3.240.2194530.18749508X-RAY DIFFRACTION100
3.24-3.340.24594800.20029437X-RAY DIFFRACTION99.99
3.34-3.460.22665260.19819370X-RAY DIFFRACTION100
3.46-3.60.21885300.18459469X-RAY DIFFRACTION100
3.6-3.760.20124690.16819437X-RAY DIFFRACTION100
3.76-3.960.20175200.16159445X-RAY DIFFRACTION99.98
3.96-4.210.17824970.14619386X-RAY DIFFRACTION99.97
4.21-4.530.17595520.14779431X-RAY DIFFRACTION99.98
4.53-4.990.17985100.14699401X-RAY DIFFRACTION99.95
4.99-5.710.17184550.16089484X-RAY DIFFRACTION99.93
5.71-7.180.2125010.18519450X-RAY DIFFRACTION99.93
7.18-35.380.19354380.18379056X-RAY DIFFRACTION95.06

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