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- PDB-8xr2: Crystal structure of AKRtyl-apo1 -

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Basic information

Entry
Database: PDB / ID: 8xr2
TitleCrystal structure of AKRtyl-apo1
ComponentsAldo/keto reductase
KeywordsOXIDOREDUCTASE / apo structure / Aldo-keto reductase
Function / homology: / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / oxidoreductase activity / nucleotide binding / cytosol / Aldo/keto reductase
Function and homology information
Biological speciesStreptomyces xinghaiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 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
DepositionJan 6, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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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


Theoretical massNumber of molelcules
Total (without water)580,69916
Polymers580,69916
Non-polymers00
Water28,3381573
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


Theoretical massNumber of molelcules
Total (without water)290,3508
Polymers290,3508
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29220 Å2
ΔGint-94 kcal/mol
Surface area86970 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


Theoretical massNumber of molelcules
Total (without water)290,3508
Polymers290,3508
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29180 Å2
ΔGint-94 kcal/mol
Surface area86880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.780, 110.780, 561.108
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: 36293.703 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1573 / 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: 3.15 Å3/Da / Density % sol: 60.93 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 50 % v/v MPD, 0.1 M Imidazole, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97862 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 14, 2023
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97862 Å / Relative weight: 1
ReflectionResolution: 2.39→49.67 Å / Num. obs: 265114 / % possible obs: 100 % / Redundancy: 12.7 % / Biso Wilson estimate: 27.71 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.192 / Rpim(I) all: 0.057 / Net I/σ(I): 9.6
Reflection shellResolution: 2.39→2.43 Å / Rmerge(I) obs: 0.711 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 13176 / CC1/2: 0.832 / Rpim(I) all: 0.287

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-30007.21data reduction
HKL-30007.21data scaling
PHASER2.7.0phasing
PDB_EXTRACT4.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.39→49.67 Å / SU ML: 0.3395 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.6165
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2629 13198 4.99 %RANDOM
Rwork0.2217 251543 --
obs0.2237 264741 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.13 Å2
Refinement stepCycle: LAST / Resolution: 2.39→49.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms38119 0 0 1573 39692
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008838925
X-RAY DIFFRACTIONf_angle_d1.030252817
X-RAY DIFFRACTIONf_chiral_restr0.06135748
X-RAY DIFFRACTIONf_plane_restr0.00616949
X-RAY DIFFRACTIONf_dihedral_angle_d31.381114162
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.420.33694640.2698428X-RAY DIFFRACTION100
2.42-2.450.31274970.25668308X-RAY DIFFRACTION100
2.45-2.480.30683900.24798422X-RAY DIFFRACTION100
2.48-2.510.32414360.25368407X-RAY DIFFRACTION99.99
2.51-2.540.29954440.24018333X-RAY DIFFRACTION100
2.54-2.570.32714110.2518479X-RAY DIFFRACTION100
2.57-2.610.31273630.24718484X-RAY DIFFRACTION100
2.61-2.650.29234620.22678301X-RAY DIFFRACTION100
2.65-2.690.28094340.22538443X-RAY DIFFRACTION100
2.69-2.740.28834200.23668346X-RAY DIFFRACTION99.99
2.74-2.780.29894440.23728435X-RAY DIFFRACTION99.98
2.78-2.830.28114410.23518364X-RAY DIFFRACTION100
2.83-2.890.28634260.23428343X-RAY DIFFRACTION99.99
2.89-2.950.30874260.24498448X-RAY DIFFRACTION100
2.95-3.010.28113990.23728430X-RAY DIFFRACTION100
3.01-3.080.2744490.22688382X-RAY DIFFRACTION100
3.08-3.160.26634520.22868377X-RAY DIFFRACTION100
3.16-3.240.28354380.22918397X-RAY DIFFRACTION100
3.24-3.340.27124750.22568314X-RAY DIFFRACTION100
3.34-3.450.27834120.22818457X-RAY DIFFRACTION100
3.45-3.570.26115130.21778333X-RAY DIFFRACTION100
3.57-3.710.26884930.21598280X-RAY DIFFRACTION100
3.71-3.880.2464380.20498401X-RAY DIFFRACTION100
3.88-4.090.22364940.19838338X-RAY DIFFRACTION99.98
4.09-4.340.22784350.19598397X-RAY DIFFRACTION100
4.34-4.680.21954260.19358400X-RAY DIFFRACTION99.99
4.68-5.150.22284550.20178388X-RAY DIFFRACTION99.97
5.15-5.890.24094410.21648416X-RAY DIFFRACTION99.98
5.89-7.420.25824230.2358430X-RAY DIFFRACTION99.93
7.42-49.670.21943970.21128262X-RAY DIFFRACTION97.46

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