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- PDB-29nt: Structure of old yellow enzyme (Kluyveromyces marxianus) at 1.7 A... -

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Basic information

Entry
Database: PDB / ID: 29nt
TitleStructure of old yellow enzyme (Kluyveromyces marxianus) at 1.7 Angstroms resolution | Mutant Y200F
ComponentsEnoate reductase 1
KeywordsOXIDOREDUCTASE / Reductase / ERED / FMN
Function / homologyNADPH dehydrogenase activity / Oxidoreductase Oye-like / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / FMN binding / Aldolase-type TIM barrel / apoptotic process / FLAVIN MONONUCLEOTIDE / Enoate reductase 1
Function and homology information
Biological speciesKluyveromyces marxianus (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMolbitz, J. / Guardado Calvo, P. / Sanchez Lopez, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
University of Cambridge225914/Z/22/Z United Kingdom
CitationJournal: To Be Published
Title: Structure of old yellow enzyme (Kluyveromyces marxianus) at 1.7 Angstroms resolution | Mutant Y200F
Authors: Molbitz, J. / Guardado Calvo, P. / Sanchez Lopez, M.
History
DepositionMar 24, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 21, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Enoate reductase 1
B: Enoate reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,9397
Polymers91,7382
Non-polymers1,2015
Water20,4831137
1
A: Enoate reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4223
Polymers45,8691
Non-polymers5522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Enoate reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5184
Polymers45,8691
Non-polymers6483
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.485, 83.739, 205.611
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1(chain "A" and (resid 5 through 32 or resid 34...
d_2ens_1(chain "B" and (resid 5 through 32 or resid 34 through 316 or resid 318 through 402))

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11GLUGLULEULEUAA5 - 3218 - 45
d_12ASNASNALAALAAA34 - 29447 - 307
d_13LYSLYSTYRTYRAA307 - 316320 - 329
d_14VALVALVALVALAA318 - 402331 - 415
d_21GLUGLULEULEUBB5 - 3218 - 45
d_22ASNASNTYRTYRBB34 - 31647 - 329
d_23VALVALVALVALBB318 - 402331 - 415

NCS oper: (Code: givenMatrix: (-0.82956010714882, -0.26357619248398, -0.49229830325006), (-0.24739105679585, -0.61689167353146, 0.74715616048118), (-0.50062730013921, 0.74160114204551, 0. ...NCS oper: (Code: given
Matrix: (-0.82956010714882, -0.26357619248398, -0.49229830325006), (-0.24739105679585, -0.61689167353146, 0.74715616048118), (-0.50062730013921, 0.74160114204551, 0.44654232998914)
Vector: -2.6523950458077, -8.6479680089563, 3.6534785112804)

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Components

#1: Protein Enoate reductase 1


Mass: 45869.191 Da / Num. of mol.: 2 / Mutation: Y200F
Source method: isolated from a genetically manipulated source
Details: N-terminal 6X histidine fusion tag / Source: (gene. exp.) Kluyveromyces marxianus (yeast) / Gene: KYE1, FIM1_248 / Plasmid: pET-28.a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0ABX6EPS5
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1137 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.42 Å3/Da / Density % sol: 49.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2 M KNaTartrate, 0.1 M Na3Citrate, 2 M (NH4)2SO4, pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 3, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.7→46.03 Å / Num. obs: 98923 / % possible obs: 99.8 % / Redundancy: 13.6 % / Biso Wilson estimate: 21.75 Å2 / CC1/2: 0.999 / Net I/σ(I): 19.2
Reflection shellResolution: 1.7→1.72 Å / Redundancy: 13.2 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4724 / CC1/2: 0.631 / % possible all: 97.15

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Processing

Software
NameVersionClassification
PHENIX2.0_5936refinement
XDS20250430data reduction
Aimless0.8.2data scaling
PHENIX2.0_5936phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→46.03 Å / SU ML: 0.1955 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.0977
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1979 4946 5.01 %
Rwork0.1604 93859 -
obs0.1623 98805 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.44 Å2
Refinement stepCycle: LAST / Resolution: 1.7→46.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6044 0 77 1137 7258
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02036284
X-RAY DIFFRACTIONf_angle_d1.51218525
X-RAY DIFFRACTIONf_chiral_restr0.1115907
X-RAY DIFFRACTIONf_plane_restr0.01641117
X-RAY DIFFRACTIONf_dihedral_angle_d16.13132297
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.68627498048096 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.36491480.28152999X-RAY DIFFRACTION96.15
1.72-1.740.26811800.24223046X-RAY DIFFRACTION99.97
1.74-1.760.28991580.2193099X-RAY DIFFRACTION99.94
1.76-1.780.25221630.21793109X-RAY DIFFRACTION99.39
1.78-1.80.25271600.21513059X-RAY DIFFRACTION99.97
1.8-1.830.25011550.21513110X-RAY DIFFRACTION99.88
1.83-1.860.26011680.22353100X-RAY DIFFRACTION99.48
1.86-1.880.26841390.23013103X-RAY DIFFRACTION99.78
1.88-1.910.25271640.22713105X-RAY DIFFRACTION99.73
1.91-1.940.25041520.20533106X-RAY DIFFRACTION99.97
1.94-1.980.2481840.18573092X-RAY DIFFRACTION99.91
1.98-2.010.21621560.16873078X-RAY DIFFRACTION99.85
2.01-2.050.2061560.15823149X-RAY DIFFRACTION100
2.05-2.090.20321700.16423092X-RAY DIFFRACTION99.97
2.09-2.140.20361770.16343131X-RAY DIFFRACTION100
2.14-2.190.18991730.15883068X-RAY DIFFRACTION99.97
2.19-2.240.21011610.15753139X-RAY DIFFRACTION100
2.24-2.310.19311520.15553111X-RAY DIFFRACTION100
2.31-2.370.20251740.14943132X-RAY DIFFRACTION100
2.37-2.450.18361660.14673150X-RAY DIFFRACTION100
2.45-2.540.1771470.14643129X-RAY DIFFRACTION100
2.54-2.640.19971720.14653113X-RAY DIFFRACTION100
2.64-2.760.19911720.14753134X-RAY DIFFRACTION100
2.76-2.90.17031620.14713179X-RAY DIFFRACTION100
2.9-3.090.18581820.14913151X-RAY DIFFRACTION100
3.09-3.320.1961720.15363144X-RAY DIFFRACTION99.97
3.32-3.660.17891650.14783215X-RAY DIFFRACTION99.82
3.66-4.190.16541580.13283198X-RAY DIFFRACTION100
4.19-5.270.14691700.1323248X-RAY DIFFRACTION99.97
5.28-46.030.22141900.18623370X-RAY DIFFRACTION98.97

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