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- PDB-3wcz: Crystal structure of Bombyx mori aldo-keto reductase (AKR2E4) in ... -

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Basic information

Entry
Database: PDB / ID: 3wcz
TitleCrystal structure of Bombyx mori aldo-keto reductase (AKR2E4) in complex with NADP
ComponentsAldo-keto reductase 2E
KeywordsOXIDOREDUCTASE / TIM-BARREL / REDUCTASE / NADP / CYTOSOL
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / steroid metabolic process / oxidoreductase activity
Similarity search - Function
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 ...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
CITRIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Aldo-keto reductase AKR2E4
Similarity search - Component
Biological speciesBombyx mori (domestic silkworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsYamamoto, K. / Wilson, D.K.
CitationJournal: Arch.Biochem.Biophys. / Year: 2013
Title: Identification, characterization, and crystal structure of an aldo-keto reductase (AKR2E4) from the silkworm Bombyx mori.
Authors: Yamamoto, K. / Wilson, D.K.
History
DepositionJun 5, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 1, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aldo-keto reductase 2E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5697
Polymers34,3861
Non-polymers1,1846
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.089, 55.359, 59.197
Angle α, β, γ (deg.)90.00, 106.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Aldo-keto reductase 2E / Uncharacterized protein


Mass: 34385.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Gene: akr2e / Production host: Escherichia coli (E. coli) / References: UniProt: H9JTG9
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.1 Å3/Da / Density % sol: 41.5 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1M SODIUM CITRATE, 0.1M CACODYLATE (PH 6.5), VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.3→34.503 Å / Num. obs: 69041 / % possible obs: 98.5 % / Observed criterion σ(I): 3
Reflection shellHighest resolution: 1.3 Å / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(PHENIX.REFINE: 1.7.1_743)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HDJ

2hdj


Resolution: 1.3→34.5 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 16.65 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.164 2000 2.9 %
Rwork0.151 --
obs0.152 69008 98.4 %
Solvent computationShrinkage radii: 0.17 Å / VDW probe radii: 0.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45 Å2 / ksol: 0.5 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.8581 Å2-0 Å2-0.2779 Å2
2---3.0548 Å20 Å2
3----0.8032 Å2
Refinement stepCycle: LAST / Resolution: 1.3→34.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2417 0 77 237 2731
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122586
X-RAY DIFFRACTIONf_angle_d1.5023535
X-RAY DIFFRACTIONf_dihedral_angle_d16.867964
X-RAY DIFFRACTIONf_chiral_restr0.25394
X-RAY DIFFRACTIONf_plane_restr0.009463
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.3001-1.33260.30581220.2897409885
1.3326-1.36860.27731390.2405461896
1.3686-1.40890.19561450.1974857100
1.4089-1.45440.24051430.18174826100
1.4544-1.50640.17841440.16494824100
1.5064-1.56670.19961440.15554829100
1.5667-1.6380.17821460.14544855100
1.638-1.72430.15841430.14094834100
1.7243-1.83240.16571450.13794837100
1.8324-1.97380.14971450.13974848100
1.9738-2.17240.15661440.13494848100
2.1724-2.48670.14491450.13624879100
2.4867-3.13270.15191470.14094896100
3.1327-34.51550.14011480.14944959100

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