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- PDB-7ve7: Crystal structure of KRED mutant-F147L/L153Q/Y190P/L199A/M205F/M206F -

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Basic information

Entry
Database: PDB / ID: 7ve7
TitleCrystal structure of KRED mutant-F147L/L153Q/Y190P/L199A/M205F/M206F
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: 1.72000696882 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 8, 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)110,11510
Polymers107,0934
Non-polymers3,0226
Water6,702372
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 area19140 Å2
ΔGint-107 kcal/mol
Surface area29570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.310, 55.570, 128.560
Angle α, β, γ (deg.)90.000, 103.890, 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.: 2 / Source method: isolated from a natural source / Formula: Mg
#3: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 372 / 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: 2.09 Å3/Da / Density % sol: 41.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Bis-Tris pH 6.5, 25% (w/v) PEG3350, 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: 1.72→23.84 Å / Num. obs: 93405 / % possible obs: 99.7 % / Redundancy: 6.6 % / Biso Wilson estimate: 29.5105622665 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.028 / Rrim(I) all: 0.071 / Net I/σ(I): 13.9
Reflection shellResolution: 1.72→1.76 Å / Redundancy: 7 % / Rmerge(I) obs: 1.018 / Num. unique obs: 6873 / CC1/2: 0.836 / Rpim(I) all: 0.413 / Rrim(I) all: 1.1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RF2

4rf2


Resolution: 1.72000696882→21.3270754494 Å / SU ML: 0.192447001479 / Cross valid method: FREE R-VALUE / σ(F): 1.34760516911 / Phase error: 24.5983880853
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.209694417468 4703 5.03970252575 %
Rwork0.173649289 88616 -
obs0.175432672799 93319 99.6359171471 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.1814740486 Å2
Refinement stepCycle: LAST / Resolution: 1.72000696882→21.3270754494 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7414 0 194 372 7980
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005349298820697752
X-RAY DIFFRACTIONf_angle_d0.91294191678610547
X-RAY DIFFRACTIONf_chiral_restr0.0584684533991216
X-RAY DIFFRACTIONf_plane_restr0.004661284474591350
X-RAY DIFFRACTIONf_dihedral_angle_d10.27595347444937
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.720007-1.73950.354623063141440.3098457591052979X-RAY DIFFRACTION99.8401534527
1.7395-1.760.3459355636771780.2913977377572911X-RAY DIFFRACTION99.8383968972
1.76-1.78150.3091770376951620.2886831557452928X-RAY DIFFRACTION99.6774193548
1.7815-1.8040.2566554601781590.2650103114862912X-RAY DIFFRACTION99.6754300552
1.804-1.82770.2911933244651480.2392807500022942X-RAY DIFFRACTION100
1.8277-1.85270.2678017651811490.2463528553462975X-RAY DIFFRACTION99.968
1.8527-1.87920.2780185030761410.2330982651292942X-RAY DIFFRACTION99.8380829016
1.8792-1.90720.2289875883731460.2180986492182966X-RAY DIFFRACTION99.8075689545
1.9072-1.9370.2202036507061500.2209023954092917X-RAY DIFFRACTION99.7398373984
1.937-1.96870.2482381296791790.203186576172941X-RAY DIFFRACTION99.935938501
1.9687-2.00270.2591013461221670.1997854982922962X-RAY DIFFRACTION99.8404594767
2.0027-2.03910.239551903891570.1960362285872922X-RAY DIFFRACTION99.7408487204
2.0391-2.07820.2495833475571270.1978387727182961X-RAY DIFFRACTION99.8706338939
2.0782-2.12060.1983408506561580.1801953642032986X-RAY DIFFRACTION100
2.1206-2.16670.2083484021931770.1791261770282889X-RAY DIFFRACTION99.9348109518
2.1667-2.2170.203050922641470.1691071670152972X-RAY DIFFRACTION99.6485623003
2.217-2.27240.2010629544851560.1731888634432925X-RAY DIFFRACTION99.6764801035
2.2724-2.33380.2198601773651580.1743344697013008X-RAY DIFFRACTION99.8738170347
2.3338-2.40240.2051472738551650.1659516391042937X-RAY DIFFRACTION99.8390730608
2.4024-2.47980.2168071329671560.1783071809042914X-RAY DIFFRACTION99.8698763826
2.4798-2.56830.2078862341161650.1800029997042969X-RAY DIFFRACTION99.7136493796
2.5683-2.67090.2158291635171490.1801347314722953X-RAY DIFFRACTION99.7748472178
2.6709-2.79230.2230541405411590.1892887521752983X-RAY DIFFRACTION99.2733017378
2.7923-2.93910.2237213336261570.1831712104012934X-RAY DIFFRACTION99.3890675241
2.9391-3.12270.2099653658151750.188542968712926X-RAY DIFFRACTION99.4228919525
3.1227-3.3630.2458910094391430.1719901583422961X-RAY DIFFRACTION99.4871794872
3.363-3.69980.1867176380711590.1538732270822994X-RAY DIFFRACTION99.0574929312
3.6998-4.23160.18233265451580.1454827489752946X-RAY DIFFRACTION98.8535031847
4.2316-5.31760.1744242768311740.1412207980182993X-RAY DIFFRACTION99.5285983658
5.3176-21.30.1983609690321400.1645589194533068X-RAY DIFFRACTION98.1940618304
Refinement TLS params.Method: refined / Origin x: 30.8350315932 Å / Origin y: -31.6108450183 Å / Origin z: 31.0434383873 Å
111213212223313233
T0.191689551857 Å2-0.0204709441846 Å2-0.0224162348247 Å2-0.175091424909 Å20.00105044069686 Å2--0.213165875631 Å2
L1.08182630806 °2-0.0218818003386 °2-0.604342815628 °2-1.4166475292 °2-0.136316732208 °2--1.90601210293 °2
S0.0333578252224 Å °0.00713645077027 Å °-0.0230439169052 Å °-0.0462023147831 Å °-0.0567266628262 Å °-0.0885509638302 Å °-0.0161225574775 Å °0.150738988522 Å °0.0184571529957 Å °
Refinement TLS groupSelection details: all

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