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- PDB-6agz: Crystal structure of Old Yellow Enzyme from Pichia sp. AKU4542 -

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Basic information

Entry
Database: PDB / ID: 6agz
TitleCrystal structure of Old Yellow Enzyme from Pichia sp. AKU4542
ComponentsOld Yellow EnzymeNADPH dehydrogenase
KeywordsOXIDOREDUCTASE / TIM BARREL MOTIF / DEHYDROGENASE / FLAVOPROTEIN
Function / homologyNADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / FMN binding / Aldolase-type TIM barrel / oxidoreductase activity / FLAVIN MONONUCLEOTIDE / Old Yellow Enzyme
Function and homology information
Biological speciesPichia (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHorita, S. / Kataoka, M. / Kitamura, N. / Nakagawa, T. / Miyakawa, T. / Ohtsuka, J. / Nagata, K. / Shimizu, S. / Tanokura, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan) Japan
CitationJournal: Biosci.Biotechnol.Biochem. / Year: 2019
Title: Structural basis of different substrate preferences of two old yellow enzymes from yeasts in the asymmetric reduction of enone compounds.
Authors: Horita, S. / Kataoka, M. / Kitamura, N. / Miyakawa, T. / Ohtsuka, J. / Maejima, Y. / Shimomura, K. / Nagata, K. / Shimizu, S. / Tanokura, M.
History
DepositionAug 15, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Old Yellow Enzyme
B: Old Yellow Enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,4494
Polymers90,5362
Non-polymers9132
Water5,441302
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-12 kcal/mol
Surface area28040 Å2
2
A: Old Yellow Enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7242
Polymers45,2681
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-4 kcal/mol
Surface area14760 Å2
MethodPISA
3
B: Old Yellow Enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7242
Polymers45,2681
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-3 kcal/mol
Surface area14890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.450, 108.710, 89.930
Angle α, β, γ (deg.)90.000, 91.510, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Old Yellow Enzyme / NADPH dehydrogenase


Mass: 45268.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pichia (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5H1ZR30*PLUS
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O

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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: 2.63 Å3/Da / Density % sol: 53.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 25%(v/v) PEG 3350, 100mM Tris-HCl (pH 8.0) 200mM ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 14, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 58789 / % possible obs: 97.2 % / Redundancy: 7.4 % / Net I/σ(I): 18
Reflection shellResolution: 2→2.05 Å

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Processing

Software
NameVersionClassification
PHENIXdev_2210refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→19.69 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 24.43
RfactorNum. reflection% reflection
Rfree0.2567 2955 5.04 %
Rwork0.234 --
obs0.2351 58685 97.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 84.54 Å2 / Biso mean: 23.1055 Å2 / Biso min: 8.63 Å2
Refinement stepCycle: final / Resolution: 2→19.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6093 0 62 302 6457
Biso mean--20.1 23.35 -
Num. residues----772
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036294
X-RAY DIFFRACTIONf_angle_d0.5768528
X-RAY DIFFRACTIONf_chiral_restr0.042920
X-RAY DIFFRACTIONf_plane_restr0.0031099
X-RAY DIFFRACTIONf_dihedral_angle_d13.7243764
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.03280.25651490.23992599274897
2.0328-2.06780.29331220.2292695281799
2.0678-2.10540.26931250.23062743286899
2.1054-2.14580.3091360.23492673280999
2.1458-2.18950.3431530.25552689284299
2.1895-2.23710.41151070.44532216232381
2.2371-2.28910.50331260.47762234236083
2.2891-2.34620.32931470.282578272595
2.3462-2.40950.26781390.2326822821100
2.4095-2.48030.32681530.22326922845100
2.4803-2.56020.23081450.222227302875100
2.5602-2.65150.2541410.225226972838100
2.6515-2.75740.26161520.226527112863100
2.7574-2.88250.23851520.229827102862100
2.8825-3.0340.27391520.230427132865100
3.034-3.22330.23731490.231527182867100
3.2233-3.47090.20631260.225927272853100
3.4709-3.81790.24991380.23722680281898
3.8179-4.36510.21641540.190927272881100
4.3651-5.47990.18861460.176627312877100
5.4799-19.69130.18561430.191427852928100
Refinement TLS params.Method: refined / Origin x: 32.047 Å / Origin y: 0.3118 Å / Origin z: 99.1529 Å
111213212223313233
T0.08 Å20.0216 Å2-0.0198 Å2-0.1067 Å2-0.019 Å2--0.1303 Å2
L0.1792 °20.0881 °2-0.0644 °2-0.2778 °2-0.187 °2--1.0118 °2
S-0.015 Å °-0.02 Å °0.014 Å °0.0324 Å °-0.0361 Å °-0.0172 Å °-0.0713 Å °-0.1273 Å °0.0468 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA8 - 405
2X-RAY DIFFRACTION1allA501
3X-RAY DIFFRACTION1allB8 - 405
4X-RAY DIFFRACTION1allB501
5X-RAY DIFFRACTION1allC1 - 302

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