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- PDB-8xr4: Crystal structure of AKRtyl-NADP(H) complex -

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Basic information

Entry
Database: PDB / ID: 8xr4
TitleCrystal structure of AKRtyl-NADP(H) complex
ComponentsAldo/keto reductase
KeywordsOXIDOREDUCTASE
Function / homologyNADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / cytosol / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Aldo/keto reductase
Function and homology information
Biological speciesStreptomyces xinghaiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)296,29716
Polymers290,3508
Non-polymers5,9478
Water42,4252355
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area40250 Å2
ΔGint-123 kcal/mol
Surface area85780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.875, 197.643, 199.984
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: 36293.703 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 / Nicotinamide adenine dinucleotide phosphate


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


Mass: 18.015 Da / Num. of mol.: 2355 / 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: 2.77 Å3/Da / Density % sol: 55.52 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 18% PEG3350, 0.1 M Sodium citrate, pH 5.5

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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: 1.94→45.98 Å / Num. obs: 242437 / % possible obs: 100 % / Redundancy: 12.1 % / Biso Wilson estimate: 26.03 Å2 / CC1/2: 0.996 / Net I/σ(I): 9.6
Reflection shellResolution: 1.94→1.97 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 11892 / CC1/2: 0.82

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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: 1.94→45.98 Å / SU ML: 0.2206 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.2625
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1996 12337 5.09 %
Rwork0.1708 229942 -
obs0.1722 242279 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.31 Å2
Refinement stepCycle: LAST / Resolution: 1.94→45.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20832 0 0 2355 23187
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008221312
X-RAY DIFFRACTIONf_angle_d1.000729008
X-RAY DIFFRACTIONf_chiral_restr0.05913104
X-RAY DIFFRACTIONf_plane_restr0.00583800
X-RAY DIFFRACTIONf_dihedral_angle_d18.01687664
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.960.29644210.26027562X-RAY DIFFRACTION99.96
1.96-1.990.27484790.24117526X-RAY DIFFRACTION99.78
1.99-2.010.28264400.23957535X-RAY DIFFRACTION99.99
2.01-2.030.27333670.23297625X-RAY DIFFRACTION99.83
2.03-2.060.24554190.22327634X-RAY DIFFRACTION100
2.06-2.090.26824010.21617520X-RAY DIFFRACTION99.86
2.09-2.120.2574130.21227669X-RAY DIFFRACTION99.99
2.12-2.150.27533780.21347586X-RAY DIFFRACTION99.99
2.15-2.180.23944100.20637668X-RAY DIFFRACTION100
2.18-2.220.24064120.19867576X-RAY DIFFRACTION99.96
2.22-2.260.23344660.20017530X-RAY DIFFRACTION99.96
2.26-2.30.23414150.19397672X-RAY DIFFRACTION99.99
2.3-2.340.24193620.18967623X-RAY DIFFRACTION99.99
2.34-2.390.24213800.19237609X-RAY DIFFRACTION100
2.39-2.440.23433960.18837697X-RAY DIFFRACTION100
2.44-2.50.23364300.1877610X-RAY DIFFRACTION100
2.5-2.560.22174020.1857592X-RAY DIFFRACTION99.99
2.56-2.630.22084270.18047662X-RAY DIFFRACTION99.98
2.63-2.710.20793950.17687663X-RAY DIFFRACTION100
2.71-2.80.22754350.18437610X-RAY DIFFRACTION100
2.8-2.90.21443980.18157701X-RAY DIFFRACTION99.95
2.9-3.010.22394050.18057654X-RAY DIFFRACTION99.96
3.01-3.150.18384160.17187705X-RAY DIFFRACTION100
3.15-3.320.19734130.16967681X-RAY DIFFRACTION100
3.32-3.520.17794150.16287703X-RAY DIFFRACTION99.99
3.52-3.80.16643670.14677795X-RAY DIFFRACTION99.98
3.8-4.180.1354450.12537732X-RAY DIFFRACTION99.98
4.18-4.780.14924160.12567767X-RAY DIFFRACTION99.98
4.78-6.020.14923690.13927933X-RAY DIFFRACTION99.99
6.02-45.980.17794450.15378102X-RAY DIFFRACTION99.56

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