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- PDB-8x0j: old yellow enzymes-Q102A/Y169F/R215A/R308A -

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Basic information

Entry
Database: PDB / ID: 8x0j
Titleold yellow enzymes-Q102A/Y169F/R215A/R308A
ComponentsNADPH dehydrogenase
KeywordsOXIDOREDUCTASE / Ene reductase
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
PHOSPHATE ION / NADPH dehydrogenase
Similarity search - Component
Biological speciesGeobacillus kaustophilus HTA426 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.11 Å
AuthorsLei, W. / Wei, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Unlocking the function promiscuity of old yellow enzyme to catalyze asymmetric Morita-Baylis-Hillman reaction
Authors: Lei, W. / Wei, S.
History
DepositionNov 4, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)75,81611
Polymers74,9612
Non-polymers8559
Water00
1
A: NADPH dehydrogenase
hetero molecules

A: NADPH dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,91112
Polymers74,9612
Non-polymers95010
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-x+1/2,y,-z1
Buried area4040 Å2
ΔGint-67 kcal/mol
Surface area25190 Å2
MethodPISA
2
B: NADPH dehydrogenase
hetero molecules

B: NADPH dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,72110
Polymers74,9612
Non-polymers7608
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_554-x+1/2,y,-z-11
Buried area3750 Å2
ΔGint-62 kcal/mol
Surface area25270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.060, 143.570, 155.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-405-

PO4

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Components

#1: Protein NADPH dehydrogenase / Old yellow enzyme


Mass: 37480.543 Da / Num. of mol.: 2 / Mutation: Q102A,Y169F,R215A,R308A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus HTA426 (bacteria)
Gene: namA, GK2332 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5KXG9, NADPH dehydrogenase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: PO4
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: 3.2 Å3/Da / Density % sol: 61.6 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: glycine,PEG 2000,glycerinum

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.54178 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Jul 11, 2023 / Details: MULTILAYER
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 3.11→45.74 Å / Num. obs: 17476 / % possible obs: 98.9 % / Redundancy: 3.5 % / CC1/2: 0.967 / Rmerge(I) obs: 0.175 / Net I/σ(I): 5.8
Reflection shellResolution: 3.11→3.32 Å / Rmerge(I) obs: 0.494 / Num. unique obs: 3128

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Processing

Software
NameVersionClassification
PRIME-X5.8.0267refinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.11→45.74 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.873 / SU B: 20.894 / SU ML: 0.354 / Cross valid method: THROUGHOUT / ESU R Free: 0.476 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26484 881 5 %RANDOM
Rwork0.21513 ---
obs0.21757 17476 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.835 Å2
Baniso -1Baniso -2Baniso -3
1-4.85 Å2-0 Å20 Å2
2---1.74 Å2-0 Å2
3----3.11 Å2
Refinement stepCycle: 1 / Resolution: 3.11→45.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5270 0 45 0 5315
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0195433
X-RAY DIFFRACTIONr_bond_other_d0.0010.025099
X-RAY DIFFRACTIONr_angle_refined_deg1.4531.9647386
X-RAY DIFFRACTIONr_angle_other_deg0.726311716
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5945677
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.62223.077247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.24915865
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9831548
X-RAY DIFFRACTIONr_chiral_restr0.0590.2791
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216172
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021220
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_it1.3233.5282714
X-RAY DIFFRACTIONr_mcbond_other1.3213.5272713
X-RAY DIFFRACTIONr_mcangle_it2.3175.2873389
X-RAY DIFFRACTIONr_mcangle_other2.3175.2873390
X-RAY DIFFRACTIONr_scbond_it1.1973.7282719
X-RAY DIFFRACTIONr_scbond_other1.1453.6732684
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0225.4593944
X-RAY DIFFRACTIONr_long_range_B_refined4.7141.6516064
X-RAY DIFFRACTIONr_long_range_B_other4.70941.6516065
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 11259 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.11→3.188 Å
RfactorNum. reflection% reflection
Rfree0.345 62 -
Rwork0.322 1202 -
obs--98.6 %

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