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- PDB-8x8j: The structure of AbBioc in complex with inhibitor sinefungin -

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Basic information

Entry
Database: PDB / ID: 8x8j
TitleThe structure of AbBioc in complex with inhibitor sinefungin
ComponentsMalonyl-[acyl-carrier protein] O-methyltransferase
KeywordsTRANSFERASE / BioC methyltransferase / Druggable pathway / Biotin synthesis
Function / homology
Function and homology information


malonyl-[acyl-carrier protein] O-methyltransferase / malonyl-CoA methyltransferase activity / carboxyl-O-methyltransferase activity / biotin biosynthetic process / methylation
Similarity search - Function
Malonyl-[acyl-carrier protein] O-methyltransferase BioC / : / Methyltransferase domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
1,4-DIETHYLENE DIOXIDE / SINEFUNGIN / Malonyl-[acyl-carrier protein] O-methyltransferase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsZhang, W.Z. / Gan, J. / Feng, Y.J.
Funding support China, 1items
OrganizationGrant numberCountry
National Key Reserch & Development Program of China2023YFC2307100 China
CitationJournal: Sci Adv / Year: 2024
Title: A bacterial methyltransferase that initiates biotin synthesis, an attractive anti-ESKAPE druggable pathway.
Authors: Su, Z. / Zhang, W. / Shi, Y. / Cui, T. / Xu, Y. / Yang, R. / Huang, M. / Zhou, C. / Zhang, H. / Lu, T. / Qu, J. / He, Z.G. / Gan, J. / Feng, Y.
History
DepositionNov 27, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Malonyl-[acyl-carrier protein] O-methyltransferase
B: Malonyl-[acyl-carrier protein] O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,16913
Polymers57,5572
Non-polymers1,61111
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.699, 56.547, 70.680
Angle α, β, γ (deg.)90.00, 101.13, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-441-

HOH

21A-445-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Malonyl-[acyl-carrier protein] O-methyltransferase


Mass: 28778.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: bioC / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1E3M3A7

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Non-polymers , 5 types, 105 molecules

#2: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N7O5 / Feature type: SUBJECT OF INVESTIGATION
#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
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 1.99 Å3/Da / Density % sol: 38.12 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 1.6M Ammonium sulfate, 10% (v/v) 1,4-Dioxane, and 0.1M MES monohydrate pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Nov 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.72→57.25 Å / Num. obs: 47476 / % possible obs: 98.9 % / Redundancy: 5.8 % / CC1/2: 0.995 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.048 / Rrim(I) all: 0.116 / Χ2: 0.86 / Net I/σ(I): 8.4 / Num. measured all: 273096
Reflection shellResolution: 1.72→1.81 Å / % possible obs: 99.9 % / Redundancy: 5.8 % / Rmerge(I) obs: 1.402 / Num. measured all: 40626 / Num. unique obs: 6974 / CC1/2: 0.368 / Rpim(I) all: 0.652 / Rrim(I) all: 1.551 / Χ2: 0.76 / Net I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
PHENIX(1.19.1_4122: ???)refinement
Aimlessdata scaling
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→40.48 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2503 2314 4.9 %
Rwork0.2202 --
obs0.2217 47247 98.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.72→40.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3662 0 102 94 3858
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053850
X-RAY DIFFRACTIONf_angle_d0.7335238
X-RAY DIFFRACTIONf_dihedral_angle_d7.539551
X-RAY DIFFRACTIONf_chiral_restr0.048577
X-RAY DIFFRACTIONf_plane_restr0.005657
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.760.35911410.30142548X-RAY DIFFRACTION96
1.76-1.790.35161440.29312596X-RAY DIFFRACTION98
1.79-1.840.35961340.2882605X-RAY DIFFRACTION98
1.84-1.880.30191340.26072719X-RAY DIFFRACTION100
1.88-1.930.26661400.24612648X-RAY DIFFRACTION100
1.93-1.990.29831250.23312667X-RAY DIFFRACTION100
1.99-2.050.24761760.23052642X-RAY DIFFRACTION100
2.05-2.130.26271370.21712698X-RAY DIFFRACTION100
2.13-2.210.25941270.21152686X-RAY DIFFRACTION100
2.21-2.310.23881170.21872375X-RAY DIFFRACTION88
2.31-2.430.26781280.22142633X-RAY DIFFRACTION98
2.43-2.590.25041250.22612717X-RAY DIFFRACTION100
2.59-2.790.24891430.23462660X-RAY DIFFRACTION100
2.79-3.070.27461130.23652705X-RAY DIFFRACTION99
3.07-3.510.24031390.22082695X-RAY DIFFRACTION99
3.51-4.420.21471450.18752672X-RAY DIFFRACTION99
4.42-40.480.23121460.20352667X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 20.2816 Å / Origin y: 9.2889 Å / Origin z: 17.3914 Å
111213212223313233
T0.2254 Å2-0.0024 Å2-0.0118 Å2-0.1415 Å20.0018 Å2--0.1207 Å2
L1.1256 °20.6827 °2-0.1788 °2-1.1867 °20.0155 °2--0.6957 °2
S0.1623 Å °-0.0827 Å °-0.0488 Å °0.301 Å °-0.1343 Å °-0.0904 Å °0.0965 Å °-0.0203 Å °-0.0232 Å °
Refinement TLS groupSelection details: all

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