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- PDB-9h8q: Eugenol Oxidase (EUGO) from Rhodococcus jostii RHA1, mutant DTT-T425G -

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Basic information

Entry
Database: PDB / ID: 9h8q
TitleEugenol Oxidase (EUGO) from Rhodococcus jostii RHA1, mutant DTT-T425G
ComponentsProbable vanillyl-alcohol oxidase
KeywordsOXIDOREDUCTASE / Mutant / vanillyl alcohol oxidase / ether cleavage
Function / homology
Function and homology information


vanillyl-alcohol oxidase / vanillyl-alcohol oxidase activity / D-lactate dehydrogenase (cytochrome) activity / lactate catabolic process / 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
FLAVIN-ADENINE DINUCLEOTIDE / Probable vanillyl-alcohol oxidase
Similarity search - Component
Biological speciesRhodococcus jostii RHA1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsRozeboom, H.J. / Fraaije, M.W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Catalysis / Year: 2025
Title: Biocatalytic Cleavage of para-Acetoxy Benzyl Ethers: Application to Protecting Group Chemistry
Authors: Ashley, B. / Demingo, C. / Rozeboom, H. / Bianciardi, N. / Dunleavy, T. / Haaksma, J.J. / Guo, Y. / Fraaije, M.W.
History
DepositionOct 29, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2025Group: Database references / Structure summary / Category: citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _struct.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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)478,71828
Polymers470,5248
Non-polymers8,19420
Water54,0272999
1
A: Probable vanillyl-alcohol oxidase
B: Probable vanillyl-alcohol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,0399
Polymers117,6312
Non-polymers2,4087
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11590 Å2
ΔGint-111 kcal/mol
Surface area34040 Å2
2
C: Probable vanillyl-alcohol oxidase
D: Probable vanillyl-alcohol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,4386
Polymers117,6312
Non-polymers1,8074
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10590 Å2
ΔGint-105 kcal/mol
Surface area33830 Å2
3
E: Probable vanillyl-alcohol oxidase
F: Probable vanillyl-alcohol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,9208
Polymers117,6312
Non-polymers2,2896
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10720 Å2
ΔGint-101 kcal/mol
Surface area34730 Å2
4
G: Probable vanillyl-alcohol oxidase
H: Probable vanillyl-alcohol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,3205
Polymers117,6312
Non-polymers1,6893
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10190 Å2
ΔGint-93 kcal/mol
Surface area34170 Å2
Unit cell
Length a, b, c (Å)90.439, 110.197, 117.536
Angle α, β, γ (deg.)89.87, 89.34, 68.51
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Probable vanillyl-alcohol oxidase


Mass: 58815.496 Da / Num. of mol.: 8
Mutation: S81H, S394V, A423M, Q425G, I427T, H434Y, I445D, S518P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus jostii RHA1 (bacteria) / Gene: RHA1_ro03282 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0SBK1, vanillyl-alcohol oxidase

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Non-polymers , 5 types, 3019 molecules

#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2999 / 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: 2.3 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8 / Details: 41-46% MPD and 0.1 M bis-tris propane

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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: Sep 25, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9655 Å / Relative weight: 1
ReflectionResolution: 1.6→117.53 Å / Num. obs: 519315 / % possible obs: 93.2 % / Redundancy: 2.8 % / CC1/2: 0.995 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.052 / Rrim(I) all: 0.09 / Χ2: 1 / Net I/σ(I): 9.7 / Num. measured all: 1437509
Reflection shellResolution: 1.6→1.63 Å / % possible obs: 60.1 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.906 / Num. measured all: 41900 / Num. unique obs: 16604 / CC1/2: 0.42 / Rpim(I) all: 0.669 / Rrim(I) all: 1.132 / Χ2: 0.98 / Net I/σ(I) obs: 1.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→102.75 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.082 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19774 25315 4.9 %RANDOM
Rwork0.17728 ---
obs0.1783 493964 93.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.927 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å2-0.02 Å20.36 Å2
2---0.22 Å2-0.12 Å2
3---0.74 Å2
Refinement stepCycle: 1 / Resolution: 1.6→102.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33040 0 550 2999 36589
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01234571
X-RAY DIFFRACTIONr_bond_other_d0.0010.01631840
X-RAY DIFFRACTIONr_angle_refined_deg1.6041.82247015
X-RAY DIFFRACTIONr_angle_other_deg0.5541.75173385
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.15354210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.2595232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.777105480
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0820.24894
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0241354
X-RAY DIFFRACTIONr_gen_planes_other0.0010.028034
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3711.416837
X-RAY DIFFRACTIONr_mcbond_other1.3711.416837
X-RAY DIFFRACTIONr_mcangle_it2.0432.51321048
X-RAY DIFFRACTIONr_mcangle_other2.0432.51321049
X-RAY DIFFRACTIONr_scbond_it2.3231.67617734
X-RAY DIFFRACTIONr_scbond_other2.3231.67617731
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5612.95825968
X-RAY DIFFRACTIONr_long_range_B_refined4.89915.7239782
X-RAY DIFFRACTIONr_long_range_B_other4.81614.6139127
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 1306 -
Rwork0.29 24552 -
obs--62.57 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2912-0.0471-0.04110.11440.04920.3571-0.0080.05390.01320.0399-0.01750.0498-0.0206-0.02820.02560.0292-0.00530.01310.028-0.01340.0373-38.94816.20222.2215
20.28130.0638-0.06070.32260.0390.1896-0.01910.0334-0.0149-0.00060.0307-0.0254-0.01330.0845-0.01160.0232-0.02060.00250.0797-0.01390.0039-3.74886.5556-4.5418
30.2869-0.04120.06470.29440.04390.17370.0086-0.0353-0.02920.0347-0.00510.0927-0.0253-0.036-0.00360.0316-0.00040.00630.01880.00010.0356-55.3442-35.8947-24.9659
40.1726-0.04570.05310.3777-0.01350.10920.00040.0031-0.0081-0.00280.0052-0.0524-0.00180.0209-0.00560.0404-0.009-0.00490.0155-0.00210.0213-20.0039-36.8084-31.4511
50.240.00450.04560.0759-0.01670.21390.00610.0258-0.01340.0127-0.0156-0.00410.02590.02150.00960.0368-0.00140.00890.011-0.00620.041422.10714.4228-57.038
60.238-0.00420.06660.2963-0.04650.15790.0007-0.0048-0.0085-0.02350.00940.03020.0166-0.0489-0.01010.0304-0.00830.00040.0233-0.00640.026-13.364615.3213-62.589
70.171-0.1467-0.00210.3484-0.15780.29810.00670.0150.06-0.0068-0.0598-0.13790.02740.09180.05310.0137-0.0025-0.00310.04410.02680.0639-1.9775-46.1034-84.8693
80.1355-0.14-0.05020.5237-0.0660.2835-0.01540.03180.005-0.01150.00990.0695-0.0143-0.04540.00550.0283-0.0114-0.01710.0170.01060.0247-37.5757-44.4715-89.6497
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 526
2X-RAY DIFFRACTION2B2 - 526
3X-RAY DIFFRACTION3C2 - 526
4X-RAY DIFFRACTION4D2 - 526
5X-RAY DIFFRACTION5E2 - 526
6X-RAY DIFFRACTION6F2 - 526
7X-RAY DIFFRACTION7G2 - 526
8X-RAY DIFFRACTION8H2 - 601

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