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- PDB-7eji: Crystal structure of KRED F147L/L153Q/Y190P/L199A/M205F/M206F var... -

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Basic information

Entry
Database: PDB / ID: 7eji
TitleCrystal structure of KRED F147L/L153Q/Y190P/L199A/M205F/M206F variant and methyl methacrylate complex
Components3-alpha-(Or 20-beta)-hydroxysteroid dehydrogenase
KeywordsOXIDOREDUCTASE / Ketoreductases / NADPH-dependent / Enantioselectivity
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity / nucleotide binding / metal ion binding
Similarity search - Function
Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
2-oxidanylisoindole-1,3-dione / methyl 2-methylprop-2-enoate / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / DI(HYDROXYETHYL)ETHER / NADP-dependent (R)-specific alcohol dehydrogenase
Similarity search - Component
Biological speciesLactobacillus kefiri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56001602495 Å
AuthorsCui, J. / Huang, X. / Wang, B. / Zhao, H. / Zhou, J.
CitationJournal: Nat Catal / Year: 2022
Title: Photoinduced chemomimetic biocatalysis for enantioselective intermolecular radical conjugate addition
Authors: Huang, X. / Feng, J. / Cui, J. / Jiang, G. / Harrison, W. / Zang, X. / Zhou, J. / Wang, B. / Zhao, H.
History
DepositionApr 2, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-alpha-(Or 20-beta)-hydroxysteroid dehydrogenase
B: 3-alpha-(Or 20-beta)-hydroxysteroid dehydrogenase
C: 3-alpha-(Or 20-beta)-hydroxysteroid dehydrogenase
D: 3-alpha-(Or 20-beta)-hydroxysteroid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,62823
Polymers107,0934
Non-polymers4,53619
Water11,602644
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21320 Å2
ΔGint-90 kcal/mol
Surface area30140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.040, 55.780, 128.850
Angle α, β, γ (deg.)90.000, 103.666, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11B-415-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
3-alpha-(Or 20-beta)-hydroxysteroid dehydrogenase / NADPH dependent R-specific alcohol dehydrogenase / SDR family NAD(P)-dependent oxidoreductase


Mass: 26773.164 Da / Num. of mol.: 4 / Mutation: F147L,L153Q,Y190P,L199A, M205F, M206F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus kefiri (bacteria) / Gene: adhR, fabG3, DNL43_05835, LKE01_04370
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q6WVP7

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Non-polymers , 9 types, 663 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-J66 / 2-oxidanylisoindole-1,3-dione


Mass: 163.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H5NO3
#7: Chemical ChemComp-J69 / methyl 2-methylprop-2-enoate / methyl methacrylate


Mass: 100.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H8O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 644 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.1 Å3/Da / Density % sol: 41.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Bis-Tris pH 6.5, 25% (w/v) PEG 3350, 0.2 M MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97919 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 1.52→62.25 Å / Num. obs: 137332 / % possible obs: 99.7 % / Redundancy: 6.7 % / Biso Wilson estimate: 21.9084709456 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.032 / Net I/σ(I): 16.3
Reflection shellResolution: 1.52→1.54 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.061 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 6583 / CC1/2: 0.712 / Rpim(I) all: 0.677 / % possible all: 96.6

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RF2

4rf2


Resolution: 1.56001602495→50.6890640226 Å / SU ML: 0.17923616796 / Cross valid method: FREE R-VALUE / σ(F): 1.35011065855 / Phase error: 24.7491095516
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.213404320396 2000 1.58171537032 %
Rwork0.184740956044 124445 -
obs0.185200229813 126445 99.6610837438 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.6000927283 Å2
Refinement stepCycle: LAST / Resolution: 1.56001602495→50.6890640226 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7492 0 297 644 8433
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005615839619317972
X-RAY DIFFRACTIONf_angle_d0.97188801917910823
X-RAY DIFFRACTIONf_chiral_restr0.05866509512041230
X-RAY DIFFRACTIONf_plane_restr0.004787380902691376
X-RAY DIFFRACTIONf_dihedral_angle_d24.20243614292873
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5601-1.5990.2909090614831420.2691041328818828X-RAY DIFFRACTION99.6888197377
1.599-1.64230.3113844041421420.2531158787888866X-RAY DIFFRACTION99.9223516362
1.6423-1.69060.2879124989621420.2446877634248806X-RAY DIFFRACTION99.7102741253
1.6906-1.74520.3043478186011420.2382351294818879X-RAY DIFFRACTION99.8119052888
1.7452-1.80750.2630031828161420.2309533559998828X-RAY DIFFRACTION99.8108378769
1.8075-1.87990.2509361489151420.2272393010718845X-RAY DIFFRACTION99.777950483
1.8799-1.96550.2662138764251430.2173934779778876X-RAY DIFFRACTION99.7346013491
1.9655-2.06910.2404752562941430.2111187070368937X-RAY DIFFRACTION99.911971831
2.0691-2.19870.2684238492611430.2038624813048875X-RAY DIFFRACTION99.7787121044
2.1987-2.36850.2305416107381420.1946619600378850X-RAY DIFFRACTION99.7227459244
2.3685-2.60680.2266022574031440.190687948228947X-RAY DIFFRACTION99.8462383306
2.6068-2.9840.2157198639771430.1874107436468898X-RAY DIFFRACTION99.5047325556
2.984-3.75940.1884384546321440.1625088131028972X-RAY DIFFRACTION99.5848809264
3.7594-500.1569410239691460.1482945615339038X-RAY DIFFRACTION98.4984984985

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