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- PDB-7e3x: Crystal structure of SDR family NAD(P)-dependent oxidoreductase f... -

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Basic information

Entry
Database: PDB / ID: 7e3x
TitleCrystal structure of SDR family NAD(P)-dependent oxidoreductase from exiguobacterium
ComponentsOxidoreductase
KeywordsOXIDOREDUCTASE / mutant / short chain reductase
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Oxidoreductase
Similarity search - Component
Biological speciesExiguobacterium sp. KKBO11 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsChen, L. / Tang, J. / Yuan, S. / Zhang, F. / Chen, S.
CitationJournal: Catalysis Science And Technology / Year: 2021
Title: Structure-guided evolution of a ketoreductase forefficient and stereoselective bioreduction of bulkyalpha-aminobeta-keto esters
Authors: Tang, J. / Chen, L. / Zhang, L. / Ni, G. / Yu, J. / Wang, H. / Zhang, F. / Yuan, S. / Feng, M. / Che, S.
History
DepositionFeb 9, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 29, 2021Provider: 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: Oxidoreductase
B: Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8074
Polymers56,3202
Non-polymers1,4872
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6210 Å2
ΔGint-43 kcal/mol
Surface area18350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.464, 71.167, 115.158
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Symmetry operation#1: x,y,z
#2: x+1/2,-y,-z+1/2
#3: -x,y,-z
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Oxidoreductase


Mass: 28159.857 Da / Num. of mol.: 2 / Mutation: F88V, V127I, A138L, R142M, A190V, S193A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Exiguobacterium sp. KKBO11 (bacteria) / Gene: AYO36_14830 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A177S9P4
#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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.49 Å3/Da / Density % sol: 50.62 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Dec 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.58→50 Å / Num. obs: 17891 / % possible obs: 97.7 % / Redundancy: 4.8 % / Biso Wilson estimate: 29.57 Å2 / CC1/2: 0.948 / Net I/σ(I): 1.6
Reflection shellResolution: 2.6→2.64 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 821 / CC1/2: 0.57

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Processing

Software
NameVersionClassification
PHENIX1refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5t2u

5t2u


Resolution: 2.58→44.76 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.2548 --
Rwork0.1917 --
obs-17845 97 %
Displacement parametersBiso max: 71.02 Å2 / Biso mean: 28.0926 Å2 / Biso min: 12.48 Å2
Refinement stepCycle: LAST / Resolution: 2.58→44.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3830 0 96 48 3974
LS refinement shellResolution: 2.58→2.6693 Å
RfactorNum. reflection% reflection
Rfree0.31 --
Rwork0.24 1498 -
obs--84.46 %

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