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- PDB-8xr3: Crystal structure of AKRtyl-apo2 -

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Basic information

Entry
Database: PDB / ID: 8xr3
TitleCrystal structure of AKRtyl-apo2
ComponentsAldo/keto reductase
KeywordsOXIDOREDUCTASE / apo structure / Aldo-keto reductase
Function / homology: / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / nucleotide binding / cytosol / Aldo/keto reductase
Function and homology information
Biological speciesStreptomyces xinghaiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 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

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Assembly

Deposited unit
C: Aldo/keto reductase
A: Aldo/keto reductase


Theoretical massNumber of molelcules
Total (without water)72,5872
Polymers72,5872
Non-polymers00
Water5,350297
1
C: Aldo/keto reductase
A: Aldo/keto reductase

C: Aldo/keto reductase
A: Aldo/keto reductase

C: Aldo/keto reductase
A: Aldo/keto reductase

C: Aldo/keto reductase
A: Aldo/keto reductase


Theoretical massNumber of molelcules
Total (without water)290,3508
Polymers290,3508
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area29220 Å2
ΔGint-102 kcal/mol
Surface area89730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.325, 109.325, 140.990
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Space group name HallI4

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Components

#1: Protein Aldo/keto reductase


Mass: 36293.703 Da / Num. of mol.: 2
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.: 297 / 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: 2.9 Å3/Da / Density % sol: 57.61 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 10 % w/v PEG 4000, 10 % v/v 2-Propanol, 0.1 M Sodium HEPES, 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: Dec 3, 2023
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97862 Å / Relative weight: 1
ReflectionResolution: 2.31→86.39 Å / Num. obs: 36443 / % possible obs: 100 % / Redundancy: 13.3 % / Biso Wilson estimate: 31.93 Å2 / CC1/2: 0.997 / Net I/σ(I): 10.2
Reflection shellResolution: 2.31→2.43 Å / Num. unique obs: 5300 / CC1/2: 0.833

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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: 2.31→38.65 Å / SU ML: 0.2431 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.8897
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2186 1949 5.35 %RANDOM
Rwork0.1729 34494 --
obs0.1753 36443 99.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.44 Å2
Refinement stepCycle: LAST / Resolution: 2.31→38.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4947 0 0 297 5244
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00975057
X-RAY DIFFRACTIONf_angle_d1.46716870
X-RAY DIFFRACTIONf_chiral_restr0.0844743
X-RAY DIFFRACTIONf_plane_restr0.0089908
X-RAY DIFFRACTIONf_dihedral_angle_d31.83151834
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.31-2.360.25611410.24132446X-RAY DIFFRACTION100
2.36-2.430.24761460.22962455X-RAY DIFFRACTION100
2.43-2.50.26641440.22752456X-RAY DIFFRACTION100
2.5-2.580.2441230.19622444X-RAY DIFFRACTION100
2.58-2.670.26221260.19822497X-RAY DIFFRACTION100
2.67-2.780.24221270.18772442X-RAY DIFFRACTION100
2.78-2.90.25161410.19242480X-RAY DIFFRACTION100
2.9-3.060.23711370.18032469X-RAY DIFFRACTION100
3.06-3.250.26751360.16582450X-RAY DIFFRACTION100
3.25-3.50.2141760.1652437X-RAY DIFFRACTION100
3.5-3.850.21281380.16262455X-RAY DIFFRACTION100
3.85-4.410.19891240.14342496X-RAY DIFFRACTION100
4.41-5.550.18361640.15042463X-RAY DIFFRACTION99.96
5.56-38.650.17811260.16612504X-RAY DIFFRACTION99.43

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