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- PDB-9h8p: Eugenol Oxidase (EUGO) from Rhodococcus jostii RHA1, mutant DTT -

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Basic information

Entry
Database: PDB / ID: 9h8p
TitleEugenol Oxidase (EUGO) from Rhodococcus jostii RHA1, mutant DTT
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 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: 1.47 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 1.0Jan 29, 2025Provider: repository / Type: Initial release

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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)480,32938
Polymers470,8768
Non-polymers9,45330
Water56,7293149
1
A: Probable vanillyl-alcohol oxidase
B: Probable vanillyl-alcohol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,56312
Polymers117,7192
Non-polymers2,84410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12700 Å2
ΔGint-121 kcal/mol
Surface area33750 Å2
MethodPISA
2
C: Probable vanillyl-alcohol oxidase
D: Probable vanillyl-alcohol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,9619
Polymers117,7192
Non-polymers2,2427
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11060 Å2
ΔGint-108 kcal/mol
Surface area34080 Å2
MethodPISA
3
E: Probable vanillyl-alcohol oxidase
F: Probable vanillyl-alcohol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,16210
Polymers117,7192
Non-polymers2,4438
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11560 Å2
ΔGint-129 kcal/mol
Surface area34170 Å2
MethodPISA
4
G: Probable vanillyl-alcohol oxidase
H: Probable vanillyl-alcohol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,6437
Polymers117,7192
Non-polymers1,9245
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10540 Å2
ΔGint-98 kcal/mol
Surface area34180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.348, 110.228, 117.259
Angle α, β, γ (deg.)89.75, 89.50, 68.43
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: 58859.543 Da / Num. of mol.: 8
Mutation: S81H, S394V, A423M, Q425T, 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 , 6 types, 3179 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.: 8 / 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.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3149 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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% 2-Methyl-2,4-pentanediol (MPD, hexylene glycol) and 0.1 M bis-tris propane pH 6.8.

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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: 1.47→117.25 Å / Num. obs: 664608 / % possible obs: 92.2 % / Redundancy: 3.4 % / CC1/2: 0.973 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.089 / Rrim(I) all: 0.166 / Χ2: 1.09 / Net I/σ(I): 6 / Num. measured all: 2261502
Reflection shellResolution: 1.47→1.49 Å / % possible obs: 55 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.882 / Num. measured all: 60758 / Num. unique obs: 19673 / CC1/2: 0.47 / Rpim(I) all: 0.589 / Rrim(I) all: 1.067 / Χ2: 1.23 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.47→102.72 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.234 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16541 32658 4.9 %RANDOM
Rwork0.14923 ---
obs0.15002 631814 92.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.239 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å2-0.03 Å20.06 Å2
2---0.1 Å2-0.15 Å2
3---0.33 Å2
Refinement stepCycle: 1 / Resolution: 1.47→102.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33064 0 625 3149 36838
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01234642
X-RAY DIFFRACTIONr_bond_other_d0.0010.01631912
X-RAY DIFFRACTIONr_angle_refined_deg1.8711.82247112
X-RAY DIFFRACTIONr_angle_other_deg0.6391.75173559
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.18854206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.5015232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.575105480
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0970.24914
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0241330
X-RAY DIFFRACTIONr_gen_planes_other0.0010.028030
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_it1.2791.02216827
X-RAY DIFFRACTIONr_mcbond_other1.2791.02216827
X-RAY DIFFRACTIONr_mcangle_it1.9221.83521032
X-RAY DIFFRACTIONr_mcangle_other1.9221.83621033
X-RAY DIFFRACTIONr_scbond_it2.5711.31417815
X-RAY DIFFRACTIONr_scbond_other2.5711.31517816
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9082.28426081
X-RAY DIFFRACTIONr_long_range_B_refined512.439717
X-RAY DIFFRACTIONr_long_range_B_other4.92911.139042
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.47→1.505 Å
RfactorNum. reflection% reflection
Rfree0.288 1505 -
Rwork0.276 29469 -
obs--57.92 %
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)
10.34870.00170.02440.17110.04990.3429-0.00460.05610.02590.01160.00510.0295-0.014-0.0064-0.00050.00610.01110.0070.05270.01680.0125-38.9386.2552.109
20.37090.1256-0.09610.33910.0330.26810.00180.03630.0023-0.00270.0175-0.0472-0.02180.0772-0.01920.00440.00170.00470.10020.00720.013-3.7936.61-4.545
30.3367-0.06690.05230.38970.05920.2085-0.009-0.0148-0.06460.03880.00710.1099-0.0104-0.03970.00190.01410.01910.01940.0420.0210.0452-55.255-35.895-24.898
40.2492-0.08250.04180.4871-0.01240.15-0.00190.0087-0.0026-0.00290.0032-0.0633-0.01230.0324-0.00130.00790.00960.00610.04220.01560.017-19.974-36.9-31.344
50.31160.01850.00770.155-0.01050.234-0.00060.022-0.0238-0.0021-0.0135-0.02590.01720.00610.01410.00560.01270.00730.03950.02010.017322.33314.255-56.826
60.30920.02850.06110.4198-0.07020.2043-0.00390.0051-0.0107-0.02480.0090.05970.0238-0.0459-0.00510.00820.00790.0020.05380.01280.0141-13.04715.17-62.431
70.2976-0.18020.0510.4593-0.20420.39650.01160.06510.0932-0.0281-0.0892-0.16880.02960.11920.07760.01090.02170.00810.09430.06290.09-1.832-46.432-84.717
80.2138-0.17660.00050.7133-0.10950.3007-0.00320.0533-0.0061-0.0479-0.00260.09260.004-0.04370.00580.02020.0086-0.01150.06440.02660.0384-37.337-44.791-89.49
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 - 526

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