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- PDB-8s4p: Crystal structure of an Ene-reductase from Penicillium steckii -

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Basic information

Entry
Database: PDB / ID: 8s4p
TitleCrystal structure of an Ene-reductase from Penicillium steckii
ComponentsNADH:flavin oxidoreductase/NADH oxidase N-terminal domain-containing protein
KeywordsOXIDOREDUCTASE / wild-type / twinning
Function / homologyNADPH dehydrogenase YqjM-like / NADPH dehydrogenase activity / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / FMN binding / NADP binding / Aldolase-type TIM barrel / FLAVIN MONONUCLEOTIDE / NADH:flavin oxidoreductase/NADH oxidase N-terminal domain-containing protein
Function and homology information
Biological speciesPenicillium steckii (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsRozeboom, H.J. / Fraaije, M.W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Chembiochem / Year: 2025
Title: Recombinant production and characterization of six ene-reductases from Pencillium steckii.
Authors: Damada, P. / Rozeboom, H. / Fraaije, M.
History
DepositionFeb 22, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NADH:flavin oxidoreductase/NADH oxidase N-terminal domain-containing protein
B: NADH:flavin oxidoreductase/NADH oxidase N-terminal domain-containing protein
C: NADH:flavin oxidoreductase/NADH oxidase N-terminal domain-containing protein
D: NADH:flavin oxidoreductase/NADH oxidase N-terminal domain-containing protein
E: NADH:flavin oxidoreductase/NADH oxidase N-terminal domain-containing protein
F: NADH:flavin oxidoreductase/NADH oxidase N-terminal domain-containing protein
G: NADH:flavin oxidoreductase/NADH oxidase N-terminal domain-containing protein
H: NADH:flavin oxidoreductase/NADH oxidase N-terminal domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)366,54630
Polymers362,3148
Non-polymers4,23122
Water18,8081044
1
A: NADH:flavin oxidoreductase/NADH oxidase N-terminal domain-containing protein
B: NADH:flavin oxidoreductase/NADH oxidase N-terminal domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,6547
Polymers90,5792
Non-polymers1,0765
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7990 Å2
ΔGint-69 kcal/mol
Surface area27240 Å2
MethodPISA
2
C: NADH:flavin oxidoreductase/NADH oxidase N-terminal domain-containing protein
D: NADH:flavin oxidoreductase/NADH oxidase N-terminal domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,6077
Polymers90,5792
Non-polymers1,0285
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7400 Å2
ΔGint-53 kcal/mol
Surface area27050 Å2
MethodPISA
3
E: NADH:flavin oxidoreductase/NADH oxidase N-terminal domain-containing protein
F: NADH:flavin oxidoreductase/NADH oxidase N-terminal domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,6428
Polymers90,5792
Non-polymers1,0646
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7760 Å2
ΔGint-72 kcal/mol
Surface area27060 Å2
MethodPISA
4
G: NADH:flavin oxidoreductase/NADH oxidase N-terminal domain-containing protein
H: NADH:flavin oxidoreductase/NADH oxidase N-terminal domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,6428
Polymers90,5792
Non-polymers1,0646
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7640 Å2
ΔGint-69 kcal/mol
Surface area27260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.482, 175.292, 107.532
Angle α, β, γ (deg.)90.00, 111.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
NADH:flavin oxidoreductase/NADH oxidase N-terminal domain-containing protein


Mass: 45289.262 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium steckii (fungus) / Gene: PENSTE_c029G02105 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1V6SMJ6

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Non-polymers , 5 types, 1066 molecules

#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1044 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.48 Å3/Da / Density % sol: 50.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.16 M calcium acetate, 0.08 M sodium cacodylate, 14.4 PEG8000, 20 % glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9655 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9655 Å / Relative weight: 1
ReflectionResolution: 2.29→86.9 Å / Num. obs: 164580 / % possible obs: 99.1 % / Redundancy: 6.9 % / CC1/2: 0.991 / Rpim(I) all: 0.084 / Net I/σ(I): 8.3
Reflection shellResolution: 2.29→2.33 Å / Num. unique obs: 8106 / CC1/2: 0.724 / Rpim(I) all: 0.391

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Processing

Software
NameVersionClassification
PHENIX(1.20_4459: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.29→86.88 Å / Cross valid method: FREE R-VALUE / σ(F): 24.07 / Phase error: 29.55 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.275 8190 4.98 %
Rwork0.201 --
obs0.213 164578 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.29→86.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24719 0 267 1044 26030
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00825583
X-RAY DIFFRACTIONf_angle_d1.02134859
X-RAY DIFFRACTIONf_dihedral_angle_d7.9673497
X-RAY DIFFRACTIONf_chiral_restr0.0573849
X-RAY DIFFRACTIONf_plane_restr0.0094520
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.330.3093360.25717770X-RAY DIFFRACTION94
2.33-2.370.36373720.24917817X-RAY DIFFRACTION94
2.37-2.420.31973890.24817737X-RAY DIFFRACTION94
2.42-2.470.34114280.24267745X-RAY DIFFRACTION93
2.47-2.520.33483770.23547831X-RAY DIFFRACTION94
2.52-2.580.32233720.2357818X-RAY DIFFRACTION94
2.58-2.640.34384060.22777757X-RAY DIFFRACTION94
2.64-2.710.34453980.2357783X-RAY DIFFRACTION94
2.71-2.790.2954770.22617702X-RAY DIFFRACTION93
2.79-2.880.3513930.22437881X-RAY DIFFRACTION94
2.88-2.990.3114040.21727821X-RAY DIFFRACTION94
2.99-3.110.30893790.21477848X-RAY DIFFRACTION95
3.11-3.250.29323870.20977885X-RAY DIFFRACTION95
3.25-3.420.27324240.19527801X-RAY DIFFRACTION94
3.42-3.630.2694130.19257813X-RAY DIFFRACTION94
3.63-3.910.29044550.18677823X-RAY DIFFRACTION94
3.91-4.310.23684250.17017915X-RAY DIFFRACTION95
4.31-4.930.2264420.17067813X-RAY DIFFRACTION94
4.93-6.210.28554120.21347934X-RAY DIFFRACTION95
6.21-86.880.23674330.22517962X-RAY DIFFRACTION94

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