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- PDB-8zax: Crystal structure of a short-chain dehydrogenase from Lactobacill... -

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Basic information

Entry
Database: PDB / ID: 8zax
TitleCrystal structure of a short-chain dehydrogenase from Lactobacillus fermentum with NADPH
ComponentsSDR family oxidoreductase
KeywordsHYDROLASE / short-chain dehydrogenase / Lactobacillus fermentum
Function / homologyPKS_KR / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / oxidoreductase activity / NAD(P)-binding domain superfamily / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / SDR family oxidoreductase
Function and homology information
Biological speciesLimosilactobacillus fermentum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsWang, J.J. / Cong, L. / Wei, H.L. / Liu, W.D. / You, S.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Scholarship Council China
CitationJournal: Adv.Synth.Catal. / Year: 2024
Title: Structure-Guided Engineering of a Short-Chain Dehydrogenase LfSDR1 for Efficient Biosynthesis of (R)-9-(2-Hydroxypropyl)adenine, the Key Intermediate of Tenofovir
Authors: Wang, Q. / Cong, L. / Guo, J. / Wang, J. / Han, X. / Zhang, W. / Liu, W. / Wei, H. / You, S.
History
DepositionApr 25, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SDR family oxidoreductase
B: SDR family oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1334
Polymers52,6462
Non-polymers1,4872
Water7,692427
1
A: SDR family oxidoreductase
B: SDR family oxidoreductase
hetero molecules

A: SDR family oxidoreductase
B: SDR family oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,2658
Polymers105,2924
Non-polymers2,9744
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area17230 Å2
ΔGint-95 kcal/mol
Surface area32540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.827, 88.818, 157.371
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-554-

HOH

21B-564-

HOH

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Components

#1: Protein SDR family oxidoreductase


Mass: 26322.930 Da / Num. of mol.: 2 / Mutation: G146D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Limosilactobacillus fermentum (bacteria)
Gene: GC247_10055
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A843R2C6
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 427 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.45 Å3/Da / Density % sol: 49.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1M MES pH 6.0, 0.05M calcium chloride, 43% PEG 200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.54→30 Å / Num. obs: 71115 / % possible obs: 92.6 % / Redundancy: 19 % / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.034 / Rrim(I) all: 0.154 / Χ2: 0.674 / Net I/σ(I): 2.6 / Num. measured all: 1348050
Reflection shellResolution: 1.54→1.6 Å / Redundancy: 13.3 % / Rmerge(I) obs: 1.204 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 6829 / CC1/2: 0.813 / CC star: 0.947 / Rpim(I) all: 0.322 / Χ2: 0.462 / % possible all: 90.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.54→29.47 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.016 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24772 3467 4.9 %RANDOM
Rwork0.2174 ---
obs0.21883 67536 92.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.654 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0 Å2-0 Å2
2--0.2 Å20 Å2
3----0.15 Å2
Refinement stepCycle: 1 / Resolution: 1.54→29.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3774 0 0 427 4201
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0123842
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163640
X-RAY DIFFRACTIONr_angle_refined_deg1.0071.8165206
X-RAY DIFFRACTIONr_angle_other_deg0.3431.7578404
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3235490
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.76516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.11410644
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0570.2588
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024450
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02808
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8051.661966
X-RAY DIFFRACTIONr_mcbond_other1.8051.661966
X-RAY DIFFRACTIONr_mcangle_it2.4812.9842454
X-RAY DIFFRACTIONr_mcangle_other2.482.9832455
X-RAY DIFFRACTIONr_scbond_it3.0372.0761876
X-RAY DIFFRACTIONr_scbond_other3.0032.0731874
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4583.6792753
X-RAY DIFFRACTIONr_long_range_B_refined6.14522.3617470
X-RAY DIFFRACTIONr_long_range_B_other5.90521.7416981
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.54→1.578 Å
RfactorNum. reflection% reflection
Rfree0.341 248 -
Rwork0.348 4701 -
obs--88.36 %

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