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- PDB-9iuv: Crystal Structure of a PtOYE Mutant (ADes-5) -

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Basic information

Entry
Database: PDB / ID: 9iuv
TitleCrystal Structure of a PtOYE Mutant (ADes-5)
ComponentsNADPH dehydrogenase
KeywordsOXIDOREDUCTASE / NADPH dehydrogenase Old yellow enzyme
Function / homology
Function and homology information


NADPH dehydrogenase / NADPH dehydrogenase activity / response to toxic substance / FMN binding / NADP binding
Similarity search - Function
NADPH dehydrogenase, bacteria / NADPH dehydrogenase YqjM-like / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / Aldolase-type TIM barrel
Similarity search - Domain/homology
ACETATE ION / FLAVIN MONONUCLEOTIDE / NADPH dehydrogenase
Similarity search - Component
Biological speciesParageobacillus thermantarcticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsZheng, S. / Liu, Z. / Yu, F. / Yin, H.
Funding support China, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
Ministry of Science and Technology (MoST, China) China
CitationJournal: To Be Published
Title: Crystal Structure of a PtOYE Mutant (ADes-5)
Authors: Zheng, S. / Liu, Z. / Yu, F. / Yin, H.
History
DepositionJul 22, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NADPH dehydrogenase
B: NADPH dehydrogenase
C: NADPH dehydrogenase
D: NADPH dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,05412
Polymers151,9934
Non-polymers2,0628
Water23,1851287
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12540 Å2
ΔGint-51 kcal/mol
Surface area48340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.410, 99.290, 89.970
Angle α, β, γ (deg.)90.000, 91.890, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
NADPH dehydrogenase


Mass: 37998.195 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parageobacillus thermantarcticus (bacteria)
Gene: namA, SAMN05192569_10087
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A1I0SYV3, NADPH dehydrogenase
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1287 / Source method: isolated from a natural source / Formula: H2O
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: 2.54 Å3/Da / Density % sol: 51.54 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M Tris-HCl (pH 7), 0.2 M sodium acetate, 14% (w/v)PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 1, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.74→31.35 Å / Num. obs: 154441 / % possible obs: 99.42 % / Redundancy: 6.7 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.184 / Net I/σ(I): 11.9
Reflection shellResolution: 1.74→1.79 Å / Rmerge(I) obs: 1.602 / Num. unique obs: 11332

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.74→29.97 Å / SU ML: 0.2166 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.3653
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2131 2008 1.3 %
Rwork0.177 152395 -
obs0.1775 154403 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.06 Å2
Refinement stepCycle: LAST / Resolution: 1.74→29.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10708 0 140 1287 12135
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019311096
X-RAY DIFFRACTIONf_angle_d1.319115048
X-RAY DIFFRACTIONf_chiral_restr0.09061616
X-RAY DIFFRACTIONf_plane_restr0.01451944
X-RAY DIFFRACTIONf_dihedral_angle_d9.63311536
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.780.36211540.324410744X-RAY DIFFRACTION98.96
1.78-1.830.32871390.272410848X-RAY DIFFRACTION99
1.83-1.890.27741370.237410809X-RAY DIFFRACTION99.06
1.89-1.950.26811300.215210860X-RAY DIFFRACTION99.32
1.95-2.020.27241390.212110828X-RAY DIFFRACTION99.2
2.02-2.10.23991470.208210861X-RAY DIFFRACTION99.43
2.1-2.190.23621380.184910887X-RAY DIFFRACTION99.5
2.19-2.310.24091450.184710879X-RAY DIFFRACTION99.54
2.31-2.450.22381430.180210861X-RAY DIFFRACTION99.57
2.45-2.640.18891470.174210925X-RAY DIFFRACTION99.62
2.64-2.910.20291530.175610902X-RAY DIFFRACTION99.68
2.91-3.330.21511430.17210955X-RAY DIFFRACTION99.64
3.33-4.190.19121440.145810973X-RAY DIFFRACTION99.7
4.19-29.970.15311490.139311063X-RAY DIFFRACTION99.34

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