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- PDB-7vdo: Crystal structure of KRED F147L/L153Q/Y190P variant -

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Basic information

Entry
Database: PDB / ID: 7vdo
TitleCrystal structure of KRED F147L/L153Q/Y190P variant
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
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: 1.855715608 Å
AuthorsCui, J. / Huang, X. / Wang, B. / Zhao, H. / Zhou, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
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
DepositionSep 7, 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
D: 3-alpha-(Or 20-beta)-hydroxysteroid dehydrogenase
A: 3-alpha-(Or 20-beta)-hydroxysteroid dehydrogenase
B: 3-alpha-(Or 20-beta)-hydroxysteroid dehydrogenase
C: 3-alpha-(Or 20-beta)-hydroxysteroid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,01919
Polymers106,9054
Non-polymers3,11415
Water13,241735
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, It was already revealed that KRED are tetramers(pdb:4rf2). The sequence homology between P2-D12-2a and KRED in their paper are higher than 90%.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19990 Å2
ΔGint-113 kcal/mol
Surface area29960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.610, 55.440, 128.950
Angle α, β, γ (deg.)90.000, 103.940, 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
11D-539-

HOH

21D-581-

HOH

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Components

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Protein , 1 types, 4 molecules DABC

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


Mass: 26726.234 Da / Num. of mol.: 4
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 , 6 types, 750 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / Bis-tris methane


Mass: 209.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 735 / 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: 2.05 Å3/Da / Density % sol: 40.13 %
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: 0.97913 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97913 Å / Relative weight: 1
ReflectionResolution: 1.855→61.93 Å / Num. obs: 73460 / % possible obs: 98.8 % / Redundancy: 6.2 % / Biso Wilson estimate: 24.5825724457 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.03 / Rrim(I) all: 0.075 / Net I/σ(I): 15.4
Reflection shellResolution: 1.855→1.9 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.504 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 5113 / CC1/2: 0.822 / Rpim(I) all: 0.265 / Rrim(I) all: 0.574 / % possible all: 93.4

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Processing

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

4rf2


Resolution: 1.855715608→31.9017853489 Å / SU ML: 0.22407996231 / Cross valid method: FREE R-VALUE / σ(F): 1.34351255351 / Phase error: 21.3030434001
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.198109482186 2000 2.7232373846 %
Rwork0.157938085445 71442 -
obs0.159038385072 73442 98.7468739075 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.0898997739 Å2
Refinement stepCycle: LAST / Resolution: 1.855715608→31.9017853489 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7399 0 197 735 8331
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00624255723797774
X-RAY DIFFRACTIONf_angle_d0.95060303229910557
X-RAY DIFFRACTIONf_chiral_restr0.05790751803971221
X-RAY DIFFRACTIONf_plane_restr0.004716983833861352
X-RAY DIFFRACTIONf_dihedral_angle_d7.294364905246202
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.856-1.90210.3252723203881340.2232655872084777X-RAY DIFFRACTION93.0466085638
1.9021-1.95350.2950308306171420.2122723957685071X-RAY DIFFRACTION98.8246445498
1.9535-2.0110.2433252869941410.1899448505255043X-RAY DIFFRACTION98.6676817663
2.011-2.07590.2278361871171390.1819312612994958X-RAY DIFFRACTION96.4975388111
2.0759-2.15010.2265941532551430.1661217460575133X-RAY DIFFRACTION99.7730711044
2.1501-2.23620.2333860864771440.1683203746085143X-RAY DIFFRACTION99.7547169811
2.2362-2.33790.2470036921531430.1685407437485107X-RAY DIFFRACTION99.4883456509
2.3379-2.46110.2096127449961440.161778647195139X-RAY DIFFRACTION99.9243427274
2.4611-2.61520.22749104421440.1728585597025152X-RAY DIFFRACTION99.7551327934
2.6152-2.81710.2261292344331430.1682651232025130X-RAY DIFFRACTION99.5093413852
2.8171-3.10030.1974021982471450.1674078748655159X-RAY DIFFRACTION99.6056338028
3.1003-3.54850.1943798139671440.1504515080875153X-RAY DIFFRACTION99.4928625094
3.5485-4.46870.161259909681450.1309614079375185X-RAY DIFFRACTION99.2921013413
4.4687-31.90.1445114054111490.1399320925915292X-RAY DIFFRACTION98.855377907

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