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- PDB-8bap: Eugenol Oxidase (EUGO) from Rhodococcus jostii RHA1, eightfold mu... -

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Basic information

Entry
Database: PDB / ID: 8bap
TitleEugenol Oxidase (EUGO) from Rhodococcus jostii RHA1, eightfold mutant active on propanol syringol
ComponentsProbable vanillyl-alcohol oxidase
KeywordsOXIDOREDUCTASE / Biocatalysis / lignin / FAD / flavoenzyme
Function / homology
Function and homology information


vanillyl-alcohol oxidase / vanillyl-alcohol oxidase activity / lactate catabolic process / D-lactate dehydrogenase (cytochrome) activity / D-lactate dehydrogenase (NAD+) activity / FAD binding / metal ion binding
Similarity search - Function
FAD-linked oxidase, C-terminal / Cytokinin dehydrogenase, C-terminal domain superfamily / FAD linked oxidases, C-terminal domain / Vanillyl-alcohol oxidase, C-terminal subdomain 2 / FAD-linked oxidase-like, C-terminal / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding, type PCMH, subdomain 1 / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. ...FAD-linked oxidase, C-terminal / Cytokinin dehydrogenase, C-terminal domain superfamily / FAD linked oxidases, C-terminal domain / Vanillyl-alcohol oxidase, C-terminal subdomain 2 / FAD-linked oxidase-like, C-terminal / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding, type PCMH, subdomain 1 / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily
Similarity search - Domain/homology
Chem-55B / FLAVIN-ADENINE DINUCLEOTIDE / Probable vanillyl-alcohol oxidase
Similarity search - Component
Biological speciesRhodococcus jostii RHA1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsAlvigini, L. / Mattevi, A.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)Grant Agreement No. 837890 (SMARTBOX).European Union
CitationJournal: Acs Catalysis / Year: 2023
Title: One-Pot Biocatalytic Synthesis of rac -Syringaresinol from a Lignin-Derived Phenol.
Authors: Guo, Y. / Alvigini, L. / Saifuddin, M. / Ashley, B. / Trajkovic, M. / Alonso-Cotchico, L. / Mattevi, A. / Fraaije, M.W.
History
DepositionOct 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Advisory / Database references / Derived calculations
Category: citation / pdbx_validate_close_contact ...citation / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _citation.pdbx_database_id_DOI
Revision 1.2Dec 13, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable vanillyl-alcohol oxidase
B: Probable vanillyl-alcohol oxidase
C: Probable vanillyl-alcohol oxidase
D: Probable vanillyl-alcohol oxidase
E: Probable vanillyl-alcohol oxidase
F: Probable vanillyl-alcohol oxidase
G: Probable vanillyl-alcohol oxidase
H: Probable vanillyl-alcohol oxidase
I: Probable vanillyl-alcohol oxidase
J: Probable vanillyl-alcohol oxidase
K: Probable vanillyl-alcohol oxidase
L: Probable vanillyl-alcohol oxidase
M: Probable vanillyl-alcohol oxidase
N: Probable vanillyl-alcohol oxidase
O: Probable vanillyl-alcohol oxidase
P: Probable vanillyl-alcohol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)958,80760
Polymers942,39316
Non-polymers16,41344
Water23,1851287
1
A: Probable vanillyl-alcohol oxidase
D: Probable vanillyl-alcohol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,9119
Polymers117,7992
Non-polymers2,1127
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10100 Å2
ΔGint-91 kcal/mol
Surface area34300 Å2
MethodPISA
2
B: Probable vanillyl-alcohol oxidase
J: Probable vanillyl-alcohol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,8718
Polymers117,7992
Non-polymers2,0726
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9960 Å2
ΔGint-89 kcal/mol
Surface area34240 Å2
MethodPISA
3
C: Probable vanillyl-alcohol oxidase
H: Probable vanillyl-alcohol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,8317
Polymers117,7992
Non-polymers2,0325
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10060 Å2
ΔGint-91 kcal/mol
Surface area34110 Å2
MethodPISA
4
F: Probable vanillyl-alcohol oxidase
hetero molecules

E: Probable vanillyl-alcohol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,8718
Polymers117,7992
Non-polymers2,0726
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area9880 Å2
ΔGint-89 kcal/mol
Surface area34370 Å2
MethodPISA
5
G: Probable vanillyl-alcohol oxidase
P: Probable vanillyl-alcohol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,7916
Polymers117,7992
Non-polymers1,9924
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9880 Å2
ΔGint-83 kcal/mol
Surface area34170 Å2
MethodPISA
6
I: Probable vanillyl-alcohol oxidase
O: Probable vanillyl-alcohol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,8317
Polymers117,7992
Non-polymers2,0325
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9900 Å2
ΔGint-82 kcal/mol
Surface area34180 Å2
MethodPISA
7
K: Probable vanillyl-alcohol oxidase
N: Probable vanillyl-alcohol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,8317
Polymers117,7992
Non-polymers2,0325
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9980 Å2
ΔGint-80 kcal/mol
Surface area34400 Å2
MethodPISA
8
L: Probable vanillyl-alcohol oxidase
M: Probable vanillyl-alcohol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,8718
Polymers117,7992
Non-polymers2,0726
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9900 Å2
ΔGint-80 kcal/mol
Surface area34490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.556, 142.995, 154.600
Angle α, β, γ (deg.)114.870, 97.000, 93.280
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Probable vanillyl-alcohol oxidase


Mass: 58899.574 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus jostii RHA1 (bacteria) / Strain: RHA1 / Gene: RHA1_ro03282 / Production host: Escherichia coli (E. coli) / Strain (production host): Top10 / References: UniProt: Q0SBK1, vanillyl-alcohol oxidase
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical
ChemComp-55B / 4-[(1E)-3-hydroxyprop-1-en-1-yl]-2,6-dimethoxyphenol / Sinapyl alcohol / sinapoyl alcohol


Mass: 210.226 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C11H14O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1287 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.39 Å3/Da / Density % sol: 48.45 %
Crystal growTemperature: 293 K / Method: batch mode / Details: Morpheus screening, condition A6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.000002 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000002 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 379398 / % possible obs: 98.2 % / Redundancy: 3.5 % / CC1/2: 0.987 / Rmerge(I) obs: 0.137 / Net I/σ(I): 4.6
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 0.707 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 18712 / CC1/2: 0.537 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX1.16_3546refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FXD

5fxd


Resolution: 2.3→49.044 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 25.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2494 18986 5 %
Rwork0.1928 360370 -
obs0.1956 379356 98.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 117.67 Å2 / Biso mean: 34.5075 Å2 / Biso min: 8.69 Å2
Refinement stepCycle: final / Resolution: 2.3→49.044 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms66160 0 1100 1287 68547
Biso mean--29.79 32.95 -
Num. residues----8400
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3-2.32610.35376590.27741187798
2.3261-2.35350.34015840.26971199398
2.3535-2.38220.30735840.25891199698
2.3822-2.41240.33446580.25421199698
2.4124-2.44410.31046460.25241187498
2.4441-2.47760.30656080.24591202098
2.4776-2.5130.33846620.26041198098
2.513-2.55050.31866270.24061195498
2.5505-2.59030.30666620.23451195298
2.5903-2.63280.31156100.24011203598
2.6328-2.67820.30736210.23991203398
2.6782-2.72690.30926430.2341199098
2.7269-2.77930.30776570.23611205298
2.7793-2.83610.30176270.22261199298
2.8361-2.89770.29346740.21621203398
2.8977-2.96510.27596360.21421201298
2.9651-3.03930.27366380.20721207598
3.0393-3.12140.28376390.21741204199
3.1214-3.21330.28886510.21131203099
3.2133-3.31690.27726010.20151212899
3.3169-3.43550.25276140.19131211799
3.4355-3.5730.2436260.18621202399
3.573-3.73550.23256490.1751202698
3.7355-3.93240.2256150.16951208998
3.9324-4.17870.19935920.15221208098
4.1787-4.50110.19616450.14981199298
4.5011-4.95370.18546290.14191201998
4.9537-5.66960.20886210.15891207499
5.6696-7.13950.18886810.15731202199
7.1395-49.0440.15886270.14671186697

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