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- PDB-9udd: Crystal structure of MonCI in complex with monoepoxidized farnesy... -

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Basic information

Entry
Database: PDB / ID: 9udd
TitleCrystal structure of MonCI in complex with monoepoxidized farnesyl acetate
ComponentsMonCI
KeywordsFLAVOPROTEIN / FAD dependent monooxygenase / epoxidase / mutant
Function / homologyFAD-dependent oxidoreductase 2, FAD binding domain / FAD binding domain / FAD/NAD(P)-binding domain superfamily / oxidoreductase activity / nucleotide binding / FLAVIN-ADENINE DINUCLEOTIDE / : / MonCI
Function and homology information
Biological speciesStreptomyces virginiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsXiao, H.L. / Guan, Y.Z. / Chen, X.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFC2106100 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2025
Title: Mechanistic and molecular insights into iterative triepoxidation catalyzed by monooxygenase MonCI using a natural substrate analog.
Authors: Deng, Y. / Guan, Y. / Xiao, H. / Kang, Y. / Dang, D. / Jiang, G. / Wang, Q. / Yang, Y. / Cheng, L. / Zang, Y. / Zhang, S. / He, W. / Hotta, K. / Liu, J.Q. / Yang, Z. / Chen, X.
History
DepositionApr 6, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 21, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MonCI
B: MonCI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,3018
Polymers110,2302
Non-polymers2,0716
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
ΔGint-24 kcal/mol
Surface area36490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.829, 52.443, 145.511
Angle α, β, γ (deg.)90.00, 92.62, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein MonCI / Monensin epoxidase


Mass: 55115.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces virginiae (bacteria) / Gene: monC1, monCI / Production host: Escherichia coli (E. coli) / References: UniProt: Q846W9

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Non-polymers , 5 types, 221 molecules

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


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-YGK / Monoepoxidized farnesyl acetate / [(2~{E},6~{E})-9-[(2~{R})-3,3-dimethyloxiran-2-yl]-3,7-dimethyl-nona-2,6-dienyl] ethanoate


Mass: 280.402 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H28O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.31 Å3/Da / Density % sol: 46.77 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion
Details: 0.1 M Lithium Chloride, 0.1 M HEPES, pH 7.3, 28%(w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.1→49.33 Å / Num. obs: 58988 / % possible obs: 99.5 % / Redundancy: 6.4 % / CC1/2: 0.993 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.052 / Rrim(I) all: 0.133 / Net I/σ(I): 8.5
Reflection shellResolution: 2.1→2.16 Å / Rmerge(I) obs: 0.672 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4346 / CC1/2: 0.77 / Rpim(I) all: 0.322 / Rrim(I) all: 0.749 / % possible all: 95.5

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Processing

Software
NameVersionClassification
PHENIX(1.16_3549: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8T3P

8t3p


Resolution: 2.1→36.34 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2311 2868 4.87 %
Rwork0.1963 --
obs0.198 58951 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→36.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7160 0 139 215 7514
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097460
X-RAY DIFFRACTIONf_angle_d1.0910180
X-RAY DIFFRACTIONf_dihedral_angle_d34.6342712
X-RAY DIFFRACTIONf_chiral_restr0.0651156
X-RAY DIFFRACTIONf_plane_restr0.0081340
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.13620.27221230.26292589X-RAY DIFFRACTION93
2.1362-2.17510.28941410.25442808X-RAY DIFFRACTION99
2.1751-2.21690.26911370.24512752X-RAY DIFFRACTION100
2.2169-2.26210.23451410.23152763X-RAY DIFFRACTION99
2.2621-2.31130.25151700.23032799X-RAY DIFFRACTION100
2.3113-2.36510.27251530.22672774X-RAY DIFFRACTION100
2.3651-2.42420.26611470.22442780X-RAY DIFFRACTION100
2.4242-2.48970.2961520.22092807X-RAY DIFFRACTION100
2.4897-2.5630.22871230.21712803X-RAY DIFFRACTION100
2.563-2.64570.26481400.20622801X-RAY DIFFRACTION100
2.6457-2.74020.2151420.20222801X-RAY DIFFRACTION100
2.7402-2.84990.2061370.19622816X-RAY DIFFRACTION100
2.8499-2.97950.22881370.20822809X-RAY DIFFRACTION100
2.9795-3.13650.24751480.20252829X-RAY DIFFRACTION100
3.1365-3.33290.23621500.20152819X-RAY DIFFRACTION100
3.3329-3.590.23391280.19892844X-RAY DIFFRACTION100
3.59-3.95090.2091320.19172841X-RAY DIFFRACTION100
3.9509-4.52170.22111510.17462842X-RAY DIFFRACTION100
4.5217-5.69340.21811540.17882877X-RAY DIFFRACTION100
5.6934-36.340.21851620.1742929X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 13.9824 Å / Origin y: -6.8127 Å / Origin z: 39.2822 Å
111213212223313233
T0.3319 Å20.0184 Å20.0098 Å2-0.3094 Å2-0.0649 Å2--0.2913 Å2
L1.6245 °2-0.0643 °20.3155 °2-0.2844 °2-0.2145 °2--0.8791 °2
S0.1069 Å °0.4163 Å °-0.2637 Å °-0.1065 Å °-0.0121 Å °0.0005 Å °0.1734 Å °-0.0794 Å °-0.0583 Å °
Refinement TLS groupSelection details: all

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