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- PDB-6kbl: Structure-function study of AKR4C14, an aldo-keto reductase from ... -

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Basic information

Entry
Database: PDB / ID: 6kbl
TitleStructure-function study of AKR4C14, an aldo-keto reductase from Thai Jasmine rice (Oryza sativa L. ssp. Indica cv. KDML105)
ComponentsAldo-keto reductase
KeywordsOXIDOREDUCTASE / Aldo-keto reductase (AKR) / Aldehyde reductase / Aldose reductase / rice AKR / AKR4C14
Function / homology
Function and homology information


D-threo-aldose 1-dehydrogenase activity
Similarity search - Function
Aldo-keto reductase family 4C / Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / NADP-dependent oxidoreductase domain / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily ...Aldo-keto reductase family 4C / Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / NADP-dependent oxidoreductase domain / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / CACODYLATE ION / Aldo-keto reductase
Similarity search - Component
Biological speciesOryza sativa subsp. indica (long-grained rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSongsiriritthigul, C. / Narawongsanont, R. / Guan, H.H. / Chen, C.J.
Citation
Journal: Acta Crystallogr D Struct Biol / Year: 2020
Title: Structure-function study of AKR4C14, an aldo-keto reductase from Thai jasmine rice (Oryza sativa L. ssp. indica cv. KDML105).
Authors: Songsiriritthigul, C. / Narawongsanont, R. / Tantitadapitak, C. / Guan, H.H. / Chen, C.J.
#1: Journal: Protein J. / Year: 2017
Title: Characterization of AKR4C15, a Novel Member of Aldo-Keto Reductase, in Comparison with Other Rice AKR(s).
Authors: Auiyawong, B. / Narawongsanont, R. / Tantitadapitak, C.
History
DepositionJun 25, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1May 20, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aldo-keto reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0144
Polymers34,7261
Non-polymers2883
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, Dynamic light scattering revealed that the purified AKR4C14 was monodisperse with percent polydispersity of 13 and hydrodynamic diameter of the AKR4C14 was 8 nm.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-0 kcal/mol
Surface area13450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.070, 65.306, 79.065
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Aldo-keto reductase /


Mass: 34725.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. indica (long-grained rice)
Gene: AKR2, OsI_04428 / Plasmid: PET28B(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B8AC38
#2: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Sequence detailsThe amino acid residue translated from gene is Glu74. But the amino acid that be properly rebuilt ...The amino acid residue translated from gene is Glu74. But the amino acid that be properly rebuilt in the map is Ala74 (appeared in the PDB Coordinates), owing to the disorder of its side chain.

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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: 2.12 Å3/Da / Density % sol: 42.1 % / Description: Rectangular morphology
Crystal growTemperature: 277 K / Method: batch mode / pH: 6.5
Details: 0.2 M sodium acetate, 0.1 M sodium cacodylate pH 6.5, 30%(w/v) PEG 8000

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Data collection

DiffractionMean temperature: 110 K / Ambient temp details: Nitrogen stream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 21, 2016
RadiationMonochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 33541 / % possible obs: 99.1 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.275 / Net I/σ(I): 18.28
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.073 / Mean I/σ(I) obs: 4.53 / Num. unique obs: 1639 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H7U

3h7u


Resolution: 1.7→29.24 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.1935 1696 5.1 %Random
Rwork0.16552 ---
obs0.16694 31801 98.65 %-
Displacement parametersBiso mean: 20.936 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2446 0 15 204 2665
LS refinement shellResolution: 1.7→1.74 Å
RfactorNum. reflection% reflection
Rfree0.261 113 -
Rwork0.211 2172 -
obs--92.29 %

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