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- PDB-9kw6: Polyether epoxide hydrolase MonBI-MonBII complex -

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Basic information

Entry
Database: PDB / ID: 9kw6
TitlePolyether epoxide hydrolase MonBI-MonBII complex
Components(MonBI,MonBII) x 2
KeywordsHYDROLASE / Polyether
Function / homologySnoaL-like domain / SnoaL-like domain / isomerase activity / NTF2-like domain superfamily / DI(HYDROXYETHYL)ETHER / MonBI / MonBII
Function and homology information
Biological speciesStreptomyces virginiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å
AuthorsYao, M. / Oikawa, A. / Minami, A. / Ozaki, T. / Maenaka, K. / Kumeta, H. / Oikawa, H. / Ose, T.
Funding support Japan, 3items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)19H04634 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)21H01754 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)22K19282 Japan
CitationJournal: Nat.Chem. / Year: 2026
Title: A system of paired polyether epoxide hydrolases enables a mouldable enzyme for consecutive ring cyclization cascades.
Authors: Yabuno, N. / Minami, A. / Ozaki, T. / Owada, Y. / Sawada, K. / Arai, A. / Sato, S. / Sugiyama, A. / Tadokoro, T. / Aizawa, T. / Dosen, T. / Nomai, T. / Matsumaru, T. / Liu, J. / Ye, T. / ...Authors: Yabuno, N. / Minami, A. / Ozaki, T. / Owada, Y. / Sawada, K. / Arai, A. / Sato, S. / Sugiyama, A. / Tadokoro, T. / Aizawa, T. / Dosen, T. / Nomai, T. / Matsumaru, T. / Liu, J. / Ye, T. / Kodama, A. / Uchiyama, S. / Hengphasatporn, K. / Shigeta, Y. / Saio, T. / Maenaka, K. / Yao, M. / Kumeta, H. / Oikawa, H. / Ose, T.
History
DepositionDec 5, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2026Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 15, 2026Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MonBI,MonBII
B: MonBI,MonBII
C: MonBI,MonBII
D: MonBI,MonBII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,41614
Polymers133,4534
Non-polymers96310
Water2,612145
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.806, 177.677, 62.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1(chain "A" and (resid 4 through 8 or resid 10...
d_2ens_1(chain "B" and (resid 4 through 8 or resid 10...
d_3ens_1(chain "C" and (resid 4 through 8 or resid 10...
d_4ens_1(chain "D" and (resid 4 through 8 or resid 10...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11GLUGLULYSLYSAA4 - 819 - 23
d_12ARGARGLEULEUAA10 - 6325 - 78
d_13GLUGLUGLUGLUAA65 - 9880 - 113
d_14GLYGLYLEULEUAA100 - 102115 - 117
d_15ALAALAPROPROAA104 - 105119 - 120
d_16ALAALASERSERAA107 - 142122 - 157
d_17ALAALAVALVALAA167 - 197167 - 197
d_18GLUGLUGLYGLYAA199 - 203199 - 203
d_19PROPROPROPROAA205 - 206205 - 206
d_110VALVALLEULEUAA208 - 213208 - 213
d_111ARGARGASPASPAA215 - 238215 - 238
d_112PHEPHEGLNGLNAA240 - 250240 - 250
d_113PROPROPROPROAA252252
d_114PROPROGLYGLYAA254 - 271254 - 271
d_115VALVALTHRTHRAA274 - 284274 - 284
d_21GLUGLULYSLYSBB4 - 819 - 23
d_22ARGARGLEULEUBB10 - 6325 - 78
d_23GLUGLUGLUGLUBB65 - 9880 - 113
d_24GLYGLYLEULEUBB100 - 102115 - 117
d_25ALAALAPROPROBB104 - 105119 - 120
d_26ALAALASERSERBB107 - 142122 - 157
d_27ALAALAVALVALBB167 - 197167 - 197
d_28GLUGLUGLYGLYBB199 - 203199 - 203
d_29PROPROPROPROBB205 - 206205 - 206
d_210VALVALLEULEUBB208 - 213208 - 213
d_211ARGARGASPASPBB215 - 238215 - 238
d_212PHEPHEGLNGLNBB240 - 250240 - 250
d_213PROPROPROPROBB252252
d_214PROPROGLYGLYBB254 - 271254 - 271
d_215VALVALTHRTHRBB274 - 284274 - 284
d_31GLUGLULYSLYSCC4 - 819 - 23
d_32ARGARGLEULEUCC10 - 6325 - 78
d_33GLUGLUGLUGLUCC65 - 9880 - 113
d_34GLYGLYLEULEUCC100 - 102115 - 117
d_35ALAALAPROPROCC104 - 105119 - 120
d_36ALAALASERSERCC107 - 142122 - 157
d_37ALAALAVALVALCC167 - 197167 - 197
d_38GLUGLUGLYGLYCC199 - 203199 - 203
d_39PROPROPROPROCC205 - 206205 - 206
d_310VALVALLEULEUCC208 - 213208 - 213
d_311ARGARGASPASPCC215 - 238215 - 238
d_312PHEPHEGLNGLNCC240 - 250240 - 250
d_313PROPROPROPROCC252252
d_314PROPROGLYGLYCC254 - 271254 - 271
d_315VALVALTHRTHRCC274 - 284274 - 284
d_41GLUGLULYSLYSDD4 - 819 - 23
d_42ARGARGLEULEUDD10 - 6325 - 78
d_43GLUGLUGLUGLUDD65 - 9880 - 113
d_44GLYGLYLEULEUDD100 - 102115 - 117
d_45ALAALAPROPRODD104 - 105119 - 120
d_46ALAALASERSERDD107 - 142122 - 157
d_47ALAALAVALVALDD167 - 197167 - 197
d_48GLUGLUGLYGLYDD199 - 203199 - 203
d_49PROPROPROPRODD205 - 206205 - 206
d_410VALVALLEULEUDD208 - 213208 - 213
d_411ARGARGASPASPDD215 - 238215 - 238
d_412PHEPHEGLNGLNDD240 - 250240 - 250
d_413PROPROPROPRODD252252
d_414PROPROGLYGLYDD254 - 271254 - 271
d_415VALVALTHRTHRDD274 - 284274 - 284

NCS oper:
IDCodeMatrixVector
1given(0.968022189561, -0.124648297159, -0.217705862422), (-0.14832505252, -0.984270542216, -0.0959748848423), (-0.202318361284, 0.125197051645, -0.971284190619)2.06207874013, -83.2489190083, 23.8501127264
2given(-0.997075878188, 0.073550877409, 0.0207355146398), (0.069975161024, 0.987807847404, -0.139065212931), (-0.0307110725093, -0.137207598333, -0.990066111421)-62.9333194364, 4.22651744427, 18.8422820615
3given(-0.975761393646, 0.128866586618, 0.17687030707), (-0.0740585762663, -0.954993108426, 0.287234207817), (0.205924816258, 0.267173287797, 0.941389082334)-57.4937048283, -82.8742432892, 17.2732197285

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Components

#1: Protein MonBI,MonBII / Probable monensin biosynthesis isomerase


Mass: 33356.703 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces virginiae (bacteria) / Gene: monBI, monBII / Production host: Escherichia (bacteria) / References: UniProt: Q846W7, UniProt: Q846W8
#2: Protein MonBI,MonBII / Probable monensin biosynthesis isomerase


Mass: 33382.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces virginiae (bacteria) / Gene: monBI, monBII / Production host: Escherichia (bacteria) / References: UniProt: Q846W7, UniProt: Q846W8
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O
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: 2.64 Å3/Da / Density % sol: 53.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10 mM HEPES 200 mM ammonium tartrate 22% PEG2000 25% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3→47.44 Å / Num. obs: 28587 / % possible obs: 100 % / Redundancy: 7.2 % / Biso Wilson estimate: 61.16 Å2 / Rmerge(I) obs: 0.119 / Χ2: 0.729 / Net I/σ(I): 14.7
Reflection shellResolution: 3→3.05 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1392 / Χ2: 0.451 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.01→44.53 Å / SU ML: 0.3488 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.5342
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.235 1464 5.13 %
Rwork0.1756 27061 -
obs0.1786 28525 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.16 Å2
Refinement stepCycle: LAST / Resolution: 3.01→44.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8321 0 63 145 8529
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01088576
X-RAY DIFFRACTIONf_angle_d1.215611658
X-RAY DIFFRACTIONf_chiral_restr0.06291306
X-RAY DIFFRACTIONf_plane_restr0.01311545
X-RAY DIFFRACTIONf_dihedral_angle_d12.51421216
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.498141805668
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.553306258118
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.596454878371
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.01-3.120.27981450.2372528X-RAY DIFFRACTION94.45
3.12-3.250.29991340.20972660X-RAY DIFFRACTION100
3.25-3.40.25851470.20342678X-RAY DIFFRACTION100
3.4-3.570.28151390.20192677X-RAY DIFFRACTION100
3.57-3.80.24881550.17992688X-RAY DIFFRACTION100
3.8-4.090.23631750.1722675X-RAY DIFFRACTION100
4.09-4.50.22941500.15852725X-RAY DIFFRACTION100
4.5-5.150.18461380.14572741X-RAY DIFFRACTION100
5.15-6.490.24461480.18312769X-RAY DIFFRACTION100
6.49-44.530.19931330.16082920X-RAY DIFFRACTION99.54

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