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- PDB-9ude: Crystal structure of MonCI in complex with diepoxidized farnesyl ... -

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Basic information

Entry
Database: PDB / ID: 9ude
TitleCrystal structure of MonCI in complex with diepoxidized 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: 2.65 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: To Be Published
Title: Molecular insights into the tri-epoxidations mechanisms of MonCI with a natural substrate analog
Authors: Deng, Y.M. / Guan, Y.Z. / Xiao, H.L. / Kang, Y. / Liu, N. / Zhou, Q. / Zang, Y.J. / Zhang, S.L. / He, W. / Hotta, K. / Kim, C.Y. / Yang, Z.W. / Chen, X.
History
DepositionApr 6, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release

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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)112,2257
Polymers110,2302
Non-polymers1,9955
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint-27 kcal/mol
Surface area35900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.622, 52.765, 145.829
Angle α, β, γ (deg.)90.00, 92.37, 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, 58 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-YK6 / diepoxidized farnesyl acetate / [(~{E})-5-[(2~{S},3~{S})-3-[2-[(2~{R})-3,3-dimethyloxiran-2-yl]ethyl]-3-methyl-oxiran-2-yl]-3-methyl-pent-2-enyl] ethanoate


Mass: 296.402 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H28O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / 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.: 53 / 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: 2.36 Å3/Da / Density % sol: 47.84 %
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: 2.65→145.704 Å / Num. obs: 29099 / % possible obs: 96.1 % / Redundancy: 3.3 % / CC1/2: 0.989 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.083 / Rrim(I) all: 0.153 / Net I/σ(I): 7.1
Reflection shellResolution: 2.65→2.78 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.611 / Num. unique obs: 3190 / CC1/2: 0.755 / Rpim(I) all: 0.383 / Rrim(I) all: 0.723 / % possible all: 79.6

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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: 2.65→145.704 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2613 1419 4.89 %
Rwork0.1992 --
obs0.2024 29047 95.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.65→145.704 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7045 0 134 53 7232
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047334
X-RAY DIFFRACTIONf_angle_d0.75710035
X-RAY DIFFRACTIONf_dihedral_angle_d7.4025143
X-RAY DIFFRACTIONf_chiral_restr0.0551158
X-RAY DIFFRACTIONf_plane_restr0.0051318
LS refinement shellResolution: 2.65→2.75 Å
RfactorNum. reflection
Rfree0.3269 112
Rwork0.2414 -
obs-2046
Refinement TLS params.Method: refined / Origin x: 14.3577 Å / Origin y: -6.788 Å / Origin z: 39.0043 Å
111213212223313233
T0.3145 Å20.0098 Å20.0315 Å2-0.2398 Å2-0.0278 Å2--0.2865 Å2
L1.4476 °2-0.0005 °20.7154 °2-0.2509 °2-0.0785 °2--1.2917 °2
S0.1187 Å °0.2862 Å °-0.2362 Å °-0.1144 Å °0.0051 Å °-0.002 Å °0.2492 Å °-0.008 Å °-0.107 Å °
Refinement TLS groupSelection details: all

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