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- PDB-7ejh: Crystal structure of KRED mutant-F147L/L153Q/Y190P/L199A/M205F/M2... -

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Basic information

Entry
Database: PDB / ID: 7ejh
TitleCrystal structure of KRED mutant-F147L/L153Q/Y190P/L199A/M205F/M206F and 2-hydroxyisoindoline-1,3-dione 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 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NADP-dependent (R)-specific alcohol dehydrogenase
Similarity search - Component
Biological speciesLactobacillus kefiri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72883927603 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

Downloads & links

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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)110,79215
Polymers107,0934
Non-polymers3,69911
Water14,196788
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19220 Å2
ΔGint-112 kcal/mol
Surface area29390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.079, 56.128, 129.036
Angle α, β, γ (deg.)90.000, 103.757, 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

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Components

#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
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Mg
#3: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-J66 / 2-oxidanylisoindole-1,3-dione


Mass: 163.130 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C8H5NO3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 788 / 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: 2.17 Å3/Da / Density % sol: 43.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES pH 6.5, 30% (w/v) PEG 2000 MME, 0.1 M Sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97855 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97855 Å / Relative weight: 1
ReflectionResolution: 1.72→50 Å / Num. obs: 93853 / % possible obs: 98.2 % / Redundancy: 6.5 % / Biso Wilson estimate: 18.3160424274 Å2 / CC1/2: 0.914 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 23
Reflection shellResolution: 1.73→1.76 Å / Rmerge(I) obs: 0.507 / Num. unique obs: 93853 / CC1/2: 0.917 / Rsym value: 0.507

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RF2

4rf2


Resolution: 1.72883927603→41.7340655768 Å / SU ML: 0.232614047856 / Cross valid method: FREE R-VALUE / σ(F): 1.3437467371 / Phase error: 28.0584998069
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.235113616947 4290 5.0386413286 %
Rwork0.196485901834 80852 -
obs0.19849978251 85142 89.0411102164 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.9078282165 Å2
Refinement stepCycle: LAST / Resolution: 1.72883927603→41.7340655768 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7460 0 243 788 8491
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006679465763567871
X-RAY DIFFRACTIONf_angle_d0.97918294669810715
X-RAY DIFFRACTIONf_chiral_restr0.06085252594591225
X-RAY DIFFRACTIONf_plane_restr0.005303526480011367
X-RAY DIFFRACTIONf_dihedral_angle_d24.27821689252803
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72884-1.74850.314033031618910.2660066863621711X-RAY DIFFRACTION56.3301031572
1.7485-1.76910.320336095113940.2657750891451856X-RAY DIFFRACTION62.2605363985
1.7691-1.79060.3497240508421070.2592867285071884X-RAY DIFFRACTION62.8869235629
1.7906-1.81330.3153249620931070.2563588988921989X-RAY DIFFRACTION66.0157480315
1.8133-1.83720.3130232081781100.2487435037192074X-RAY DIFFRACTION69.2234548336
1.8372-1.86230.3084619280011110.2408143700152171X-RAY DIFFRACTION72.559618442
1.8623-1.88890.285941852631130.246004486612304X-RAY DIFFRACTION75.8631512869
1.8889-1.91710.315143057931160.2385814058052377X-RAY DIFFRACTION78.7677725118
1.9171-1.94710.3027741502771340.2538259339082419X-RAY DIFFRACTION80.2325581395
1.9471-1.9790.2889516601141280.2630451453852588X-RAY DIFFRACTION84.9812265332
1.979-2.01310.3125888037621390.2642829930252657X-RAY DIFFRACTION88.4530211958
2.0131-2.04970.329091509771430.2665332047522770X-RAY DIFFRACTION92.2127255461
2.0497-2.08920.310765981661530.2688852011882837X-RAY DIFFRACTION93.9070351759
2.0892-2.13180.3361145489591430.2615185314072924X-RAY DIFFRACTION97.6129853596
2.1318-2.17810.2786547164631540.2458761004442942X-RAY DIFFRACTION96.992481203
2.1781-2.22880.306870142191600.2376340613222976X-RAY DIFFRACTION98.4615384615
2.2288-2.28450.2410940962061620.2483255492112940X-RAY DIFFRACTION98.9158163265
2.2845-2.34630.2746953523981670.2323964684442997X-RAY DIFFRACTION98.7515605493
2.3463-2.41530.2841307852071520.2208630906742999X-RAY DIFFRACTION99.3066498582
2.4153-2.49330.3126609145351500.2173343947212968X-RAY DIFFRACTION98.8585922638
2.4933-2.58240.2373673884161610.2099917058913033X-RAY DIFFRACTION99.315920398
2.5824-2.68580.2530812119071470.2013270734643020X-RAY DIFFRACTION99.4973295633
2.6858-2.8080.2533773000611810.2090697395543021X-RAY DIFFRACTION99.6266334785
2.808-2.9560.2449468298731800.1977387659263004X-RAY DIFFRACTION99.7493734336
2.956-3.14110.2480970729171530.1922431295183031X-RAY DIFFRACTION99.7806330304
3.1411-3.38360.21755615751640.1850145319363017X-RAY DIFFRACTION99.9057788945
3.3836-3.72390.188910951661650.1570915309563067X-RAY DIFFRACTION99.8763906057
3.7239-4.26230.1630324932111730.1390919612343048X-RAY DIFFRACTION99.9069478908
4.2623-5.36820.1457847166451710.1214326169043063X-RAY DIFFRACTION99.9381953028
5.3682-41.70.1624281645031610.1434635578833165X-RAY DIFFRACTION99.5808383234

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