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- PDB-7e24: Crystal structure of SDR family NAD(P)-dependent oxidoreductase f... -

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Basic information

Entry
Database: PDB / ID: 7.0E+24
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 acetylicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7203 Å
AuthorsChen, L. / Tang, J. / Yuan, 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 4, 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
C: Oxidoreductase
D: Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,7908
Polymers109,8164
Non-polymers2,9744
Water1,40578
1
A: Oxidoreductase
B: Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3954
Polymers54,9082
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6270 Å2
ΔGint-45 kcal/mol
Surface area18720 Å2
MethodPISA
2
C: Oxidoreductase
D: Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3954
Polymers54,9082
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6310 Å2
ΔGint-43 kcal/mol
Surface area19140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.332, 68.664, 114.675
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Oxidoreductase


Mass: 27454.092 Da / Num. of mol.: 4
Mutation: W82L,F88V, V121A, A138L, R142M, A190V, S193A, Y201F, N204A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Exiguobacterium acetylicum (bacteria) / Gene: ker / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6BDS0
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.59 Å3/Da / Density % sol: 52.45 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Jul 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.72→34.08 Å / Num. obs: 30050 / % possible obs: 99.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 31.11 Å2 / CC1/2: 0.949 / Rmerge(I) obs: 0.186 / Rpim(I) all: 0.137 / Net I/σ(I): 6.7
Reflection shellResolution: 2.72→2.79 Å / Rmerge(I) obs: 0.534 / Num. unique obs: 2115 / CC1/2: 0.712 / Rpim(I) all: 0.513

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Processing

Software
NameVersionClassification
REFMAC5.8refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5t2u

5t2u


Resolution: 2.7203→17.2607 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2624 --RANDOM
Rwork0.2081 ---
obs-29220 98 %-
Displacement parametersBiso max: 80.56 Å2 / Biso mean: 29.838 Å2 / Biso min: 11.61 Å2
Refinement stepCycle: LAST / Resolution: 2.7203→17.2607 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7638 0 192 78 7908
LS refinement shellResolution: 2.7203→2.8435 Å
RfactorNum. reflection% reflection
Rfree0.2841 --
Rwork0.252 3384 -
obs--93.8 %

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