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- PDB-7e28: Crystal structure of SDR family NAD(P)-dependent oxidoreductase f... -

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Basic information

Entry
Database: PDB / ID: 7.0E+28
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
Biological speciesExiguobacterium acetylicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 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 5, 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


Theoretical massNumber of molelcules
Total (without water)56,3602
Polymers56,3602
Non-polymers00
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-32 kcal/mol
Surface area17620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.988, 134.969, 81.453
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-314-

HOH

21A-351-

HOH

31A-356-

HOH

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Components

#1: Protein Oxidoreductase


Mass: 28179.766 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O

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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: 2.12 Å3/Da / Density % sol: 42.01 %
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: BL18U1 / 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: 1.83→54.41 Å / Num. obs: 42165 / % possible obs: 99 % / Redundancy: 5.8 % / Biso Wilson estimate: 26.22 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.061 / Rrim(I) all: 0.151 / Net I/σ(I): 6.9
Reflection shellResolution: 1.83→1.86 Å / Rmerge(I) obs: 1.571 / Mean I/σ(I) obs: 0.3 / Num. unique obs: 1895 / CC1/2: 0.412

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 7.0E+24 / Resolution: 1.83→43.49 Å / SU ML: 0.3174 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.4401
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2635 1999 4.75 %
Rwork0.2309 40109 -
obs0.2325 42108 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.68 Å2
Refinement stepCycle: LAST / Resolution: 1.83→43.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3477 0 0 98 3575
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00773531
X-RAY DIFFRACTIONf_angle_d0.90364774
X-RAY DIFFRACTIONf_chiral_restr0.0532556
X-RAY DIFFRACTIONf_plane_restr0.0047609
X-RAY DIFFRACTIONf_dihedral_angle_d5.43512102
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.880.421300.40612613X-RAY DIFFRACTION90.95
1.88-1.930.4141360.3842721X-RAY DIFFRACTION96.1
1.93-1.980.38841420.35832852X-RAY DIFFRACTION98.75
1.98-2.050.29391430.31932876X-RAY DIFFRACTION99.9
2.05-2.120.31141430.29472860X-RAY DIFFRACTION99.83
2.12-2.210.33291430.26062851X-RAY DIFFRACTION99.73
2.21-2.310.33971420.26262868X-RAY DIFFRACTION99.7
2.31-2.430.27591450.22832890X-RAY DIFFRACTION99.84
2.43-2.580.27421440.232876X-RAY DIFFRACTION99.83
2.58-2.780.29491430.24172890X-RAY DIFFRACTION99.9
2.78-3.060.26781440.23082899X-RAY DIFFRACTION99.84
3.06-3.50.24161470.21912928X-RAY DIFFRACTION99.84
3.5-4.410.20721450.18022941X-RAY DIFFRACTION99.87
4.41-43.490.21311520.18313044X-RAY DIFFRACTION99.53

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