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- PDB-5az0: Crystal structure of aldo-keto reductase (AKR2E5) of the silkworm... -

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Basic information

Entry
Database: PDB / ID: 5az0
TitleCrystal structure of aldo-keto reductase (AKR2E5) of the silkworm, Bombyx mori
ComponentsUncharacterized protein
KeywordsOXIDOREDUCTASE / enzyme specificity / Lepidoptera
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
Aldo-keto reductase family 2E / 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 ...Aldo-keto reductase family 2E / 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 / Aldo_ket_red domain-containing protein
Similarity search - Component
Biological speciesBombyx mori (domestic silkworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsYamamoto, K. / Higashiura, A. / Suzuki, M. / Nakagawa, A.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2016
Title: Structural characterization of an aldo-keto reductase (AKR2E5) from the silkworm Bombyx mori
Authors: Yamamoto, K. / Higashiura, A. / Suzuki, M. / Shiotsuki, T. / Sugahara, R. / Fujii, T. / Nakagawa, A.
History
DepositionSep 15, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1May 18, 2016Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,41811
Polymers39,8441
Non-polymers57410
Water4,504250
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-12 kcal/mol
Surface area14080 Å2
Unit cell
Length a, b, c (Å)112.180, 112.180, 147.628
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Uncharacterized protein


Mass: 39843.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Gene: LOC101740031 / Production host: Escherichia coli (E. coli) / References: UniProt: H9JJU9
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.37 Å3/Da / Density % sol: 63.45 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 4M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.2→37 Å / Num. obs: 28491 / % possible obs: 99.8 % / Redundancy: 12.1 % / Net I/σ(I): 35.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→37 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.718 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20368 1401 4.9 %RANDOM
Rwork0.15675 ---
obs0.15905 27069 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.208 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.2→37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2591 0 37 250 2878
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0192704
X-RAY DIFFRACTIONr_bond_other_d0.0020.022574
X-RAY DIFFRACTIONr_angle_refined_deg1.9091.963671
X-RAY DIFFRACTIONr_angle_other_deg1.0735910
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5775328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.57224.851134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.62315449
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.431515
X-RAY DIFFRACTIONr_chiral_restr0.1170.2405
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213076
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02617
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.3613.2861308
X-RAY DIFFRACTIONr_mcbond_other3.3393.2761299
X-RAY DIFFRACTIONr_mcangle_it4.6694.8771620
X-RAY DIFFRACTIONr_mcangle_other4.6714.8791621
X-RAY DIFFRACTIONr_scbond_it4.0783.5931396
X-RAY DIFFRACTIONr_scbond_other4.0773.5951397
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.1135.2472048
X-RAY DIFFRACTIONr_long_range_B_refined8.0826.7523265
X-RAY DIFFRACTIONr_long_range_B_other7.95526.3223158
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.199→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 106 -
Rwork0.189 1928 -
obs--98.98 %

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