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- PDB-29ns: Structure of old yellow enzyme (Kluyveromyces marxianus) at 1.53 ... -

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Basic information

Entry
Database: PDB / ID: 29ns
TitleStructure of old yellow enzyme (Kluyveromyces marxianus) at 1.53 Angstroms resolution
ComponentsEnoate reductase 1
KeywordsOXIDOREDUCTASE / Ene-reductase / OYE / FMN cofactor
Function / homology
Function and homology information


NADPH dehydrogenase activity / FMN binding / apoptotic process
Similarity search - Function
Oxidoreductase Oye-like / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / Aldolase-type TIM barrel
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / ISOBUTYL MALONIC ACID / Enoate reductase 1
Similarity search - Component
Biological speciesKluyveromyces marxianus (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 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 (Wickerhamomyces ciferrii - Uniprot: K0K9A1) at 1.6 Angstroms resolution
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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)93,0036
Polymers91,7702
Non-polymers1,2334
Water15,457858
1
B: Enoate reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5023
Polymers45,8851
Non-polymers6172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Enoate reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5023
Polymers45,8851
Non-polymers6172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.181, 82.781, 100.843
Angle α, β, γ (deg.)90.000, 97.200, 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1(chain "A" and (resid 4 through 32 or resid 34...
d_2ens_1(chain "B" and (resid 4 through 32 or resid 34...

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_11GLUGLULEULEUAB4 - 3217 - 45
d_12ASNASNTYRTYRAB34 - 31647 - 329
d_13VALVALASNASNAB318 - 373331 - 386
d_14SERSERVALVALAB375 - 402388 - 415
d_15FMNFMNFMNFMNAE501
d_16LMLLMLLMLLMLAF502
d_21GLUGLULEULEUBA4 - 3217 - 45
d_22ASNASNTYRTYRBA34 - 31647 - 329
d_23VALVALASNASNBA318 - 373331 - 386
d_24SERSERVALVALBA375 - 402388 - 415
d_25FMNFMNFMNFMNBC501
d_26LMLLMLLMLLMLBD502

NCS oper: (Code: givenMatrix: (-0.83062610267844, 0.26238728054841, -0.49113459718863), (0.24613627813542, -0.61815739877655, -0.74652418776852), (-0.49947693653948, -0.7409685184569, 0. ...NCS oper: (Code: given
Matrix: (-0.83062610267844, 0.26238728054841, -0.49113459718863), (0.24613627813542, -0.61815739877655, -0.74652418776852), (-0.49947693653948, -0.7409685184569, 0.44887464232335)
Vector: -33.585793475425, 20.12187877448, -1.1953365407866)

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Components

#1: Protein Enoate reductase 1


Mass: 45885.191 Da / Num. of mol.: 2
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-LML / ISOBUTYL MALONIC ACID


Mass: 160.168 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H12O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 858 / 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: 2.38 Å3/Da / Density % sol: 48.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 8% w/v Tascimate, 20% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 16, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.53→43.28 Å / Num. obs: 125688 / % possible obs: 99.3 % / Redundancy: 5.1 % / Biso Wilson estimate: 13.18 Å2 / CC1/2: 0.998 / Net I/σ(I): 10.7
Reflection shellResolution: 1.53→1.55 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 6226 / CC1/2: 0.705

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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: 1.53→38.25 Å / SU ML: 0.1536 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.412
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1823 6327 5.04 %
Rwork0.1539 119318 -
obs0.1553 125645 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.58 Å2
Refinement stepCycle: LAST / Resolution: 1.53→38.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6038 0 76 858 6972
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01596300
X-RAY DIFFRACTIONf_angle_d1.3768547
X-RAY DIFFRACTIONf_chiral_restr0.0945908
X-RAY DIFFRACTIONf_plane_restr0.01541126
X-RAY DIFFRACTIONf_dihedral_angle_d17.13322309
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.73237157423733 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.53-1.550.25792300.23633935X-RAY DIFFRACTION99.43
1.55-1.570.25481950.21853962X-RAY DIFFRACTION99.93
1.57-1.580.25272050.21243977X-RAY DIFFRACTION99.98
1.58-1.60.2162090.19533991X-RAY DIFFRACTION99.95
1.6-1.630.24022130.18613939X-RAY DIFFRACTION100
1.63-1.650.19682120.17583980X-RAY DIFFRACTION99.93
1.65-1.670.22281950.17693926X-RAY DIFFRACTION99.93
1.67-1.70.22742170.17253965X-RAY DIFFRACTION100
1.7-1.720.20532020.16813975X-RAY DIFFRACTION99.88
1.72-1.750.20992290.16843937X-RAY DIFFRACTION99.95
1.75-1.780.21782310.1743961X-RAY DIFFRACTION100
1.78-1.810.2041870.17173990X-RAY DIFFRACTION99.98
1.81-1.850.2082220.15923945X-RAY DIFFRACTION99.98
1.85-1.890.20062170.15363979X-RAY DIFFRACTION99.98
1.89-1.930.19112140.15333956X-RAY DIFFRACTION99.95
1.93-1.970.17211950.14914005X-RAY DIFFRACTION99.9
1.97-2.020.19091850.14723989X-RAY DIFFRACTION100
2.02-2.080.18832010.1453975X-RAY DIFFRACTION100
2.08-2.140.17342080.14853973X-RAY DIFFRACTION100
2.14-2.210.19932180.14643979X-RAY DIFFRACTION100
2.21-2.280.15952250.14383957X-RAY DIFFRACTION99.98
2.28-2.380.15882180.14693992X-RAY DIFFRACTION99.93
2.38-2.480.19182230.14633969X-RAY DIFFRACTION99.98
2.48-2.620.17332050.15113969X-RAY DIFFRACTION100
2.62-2.780.17522290.14893973X-RAY DIFFRACTION99.93
2.78-2.990.1642250.14913998X-RAY DIFFRACTION99.95
2.99-3.290.17652130.14923976X-RAY DIFFRACTION99.93
3.29-3.770.16152190.13914006X-RAY DIFFRACTION99.91
3.77-4.750.15661940.13364033X-RAY DIFFRACTION99.83
4.75-38.250.16581910.15924106X-RAY DIFFRACTION99.58

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