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- PDB-9udb: Crystal structure of MonCI in complex with farnesyl acetate -

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Basic information

Entry
Database: PDB / ID: 9udb
TitleCrystal structure of MonCI in complex with farnesyl acetate
ComponentsMonCI
KeywordsFLAVOPROTEIN / FAD-dependent monooxygenase / epoxidation
Function / homologyFAD-dependent oxidoreductase 2, FAD binding domain / FAD binding domain / FAD/NAD(P)-binding domain superfamily / oxidoreductase activity / nucleotide binding / FLAVIN-ADENINE DINUCLEOTIDE / Chem-Y7R / MonCI
Function and homology information
Biological speciesStreptomyces virginiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDeng, Y.M. / Chen, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21807088 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)112,1016
Polymers110,2302
Non-polymers1,8714
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-25 kcal/mol
Surface area37150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.263, 52.560, 145.128
Angle α, β, γ (deg.)90.00, 92.76, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#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
#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-Y7R / (2E,6E)-3,7,11-trimethyldodeca-2,6,10-trien-1-yl acetate / (2E,6E)-farnesyl acetate


Mass: 264.403 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H28O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O
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: 2.32 Å3/Da / Density % sol: 47.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 0.2 M NaCl, 0.1 M imadazole, pH 7.5, 30% PEG8000, 10% glycerol

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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: Jun 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2→19.471 Å / Num. obs: 64592 / % possible obs: 95.1 % / Redundancy: 2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.049 / Rrim(I) all: 0.069 / Net I/σ(I): 8.6
Reflection shellResolution: 2→2.05 Å / Redundancy: 2 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4502 / CC1/2: 0.464 / Rpim(I) all: 0.17 / Rrim(I) all: 0.241 / % possible all: 94

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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→19.471 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 2.27 / Phase error: 29.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.251 3106 4.81 %
Rwork0.2194 --
obs0.2209 64566 93.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→19.471 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7146 0 126 103 7375
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047420
X-RAY DIFFRACTIONf_angle_d0.7310124
X-RAY DIFFRACTIONf_dihedral_angle_d37.362699
X-RAY DIFFRACTIONf_chiral_restr0.051151
X-RAY DIFFRACTIONf_plane_restr0.0051336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.03120.4291590.38862779X-RAY DIFFRACTION93
2.0312-2.06450.38181520.37042752X-RAY DIFFRACTION95
2.0645-2.10010.37731490.3492863X-RAY DIFFRACTION96
2.1001-2.13820.33811310.32152849X-RAY DIFFRACTION97
2.1382-2.17930.32541440.31992856X-RAY DIFFRACTION96
2.1793-2.22370.31531560.31222813X-RAY DIFFRACTION96
2.2237-2.2720.37851410.30272847X-RAY DIFFRACTION96
2.272-2.32480.32921390.28992731X-RAY DIFFRACTION92
2.3248-2.38280.30621420.26462884X-RAY DIFFRACTION97
2.3828-2.44710.26921130.26412867X-RAY DIFFRACTION96
2.4471-2.5190.29771380.25952848X-RAY DIFFRACTION95
2.519-2.60010.2591460.24822812X-RAY DIFFRACTION95
2.6001-2.69280.30411450.24112812X-RAY DIFFRACTION95
2.6928-2.80030.2891250.25232752X-RAY DIFFRACTION92
2.8003-2.92740.28581480.24612825X-RAY DIFFRACTION94
2.9274-3.08110.27951420.23472817X-RAY DIFFRACTION94
3.0811-3.27330.26631310.22152790X-RAY DIFFRACTION93
3.2733-3.52470.26761400.21472762X-RAY DIFFRACTION92
3.5247-3.87690.25751540.19362686X-RAY DIFFRACTION91
3.8769-4.43210.20771510.16862776X-RAY DIFFRACTION92
4.4321-5.56230.19531360.16792694X-RAY DIFFRACTION89
5.5623-19.4710.14871240.17212645X-RAY DIFFRACTION85
Refinement TLS params.Method: refined / Origin x: -20.0554 Å / Origin y: -7.1449 Å / Origin z: 39.0334 Å
111213212223313233
T0.3853 Å20.0022 Å20.0194 Å2-0.3541 Å2-0.0429 Å2--0.3774 Å2
L1.1997 °2-0.0125 °20.3419 °2-0.3166 °2-0.0863 °2--0.752 °2
S0.0576 Å °0.3113 Å °-0.1908 Å °-0.1484 Å °0.0114 Å °-0.0282 Å °0.1052 Å °-0.0355 Å °-0.0724 Å °
Refinement TLS groupSelection details: all

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