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- PDB-8x8i: The structure of AbBioc in complex with SAM cofactor -

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Basic information

Entry
Database: PDB / ID: 8x8i
TitleThe structure of AbBioc in complex with SAM cofactor
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
S-ADENOSYLMETHIONINE / Malonyl-[acyl-carrier protein] O-methyltransferase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 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
C: Malonyl-[acyl-carrier protein] O-methyltransferase
D: Malonyl-[acyl-carrier protein] O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,7098
Polymers115,1154
Non-polymers1,5944
Water54030
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)71.055, 57.230, 143.671
Angle α, β, γ (deg.)90.00, 101.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 28778.734 Da / Num. of mol.: 4
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
#2: Chemical
ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.48 Å3/Da / Density % sol: 50.5 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 30% (v/v) PEG 400 and 0.1M CAPS/Sodium hydroxide pH 10.5

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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 PILATUS3 6M / Detector: PIXEL / Date: Nov 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.54→70.34 Å / Num. obs: 37646 / % possible obs: 99.3 % / Redundancy: 3.2 % / CC1/2: 0.993 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.072 / Rrim(I) all: 0.13 / Χ2: 0.94 / Net I/σ(I): 9.4 / Num. measured all: 119796
Reflection shellResolution: 2.54→2.67 Å / % possible obs: 99.9 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.665 / Num. measured all: 17777 / Num. unique obs: 5458 / CC1/2: 0.682 / Rpim(I) all: 0.433 / Rrim(I) all: 0.796 / Χ2: 0.87 / Net I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.54→70.34 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2875 1895 5.04 %
Rwork0.2361 --
obs0.2388 37621 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.54→70.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7478 0 108 30 7616
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037761
X-RAY DIFFRACTIONf_angle_d0.58710530
X-RAY DIFFRACTIONf_dihedral_angle_d14.5371052
X-RAY DIFFRACTIONf_chiral_restr0.0421159
X-RAY DIFFRACTIONf_plane_restr0.0031341
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.54-2.60.35341460.31582530X-RAY DIFFRACTION100
2.6-2.670.36981210.30272544X-RAY DIFFRACTION100
2.67-2.750.34771220.28632563X-RAY DIFFRACTION100
2.75-2.840.29841290.28632556X-RAY DIFFRACTION100
2.84-2.940.35291260.27972554X-RAY DIFFRACTION99
2.94-3.060.35891530.27582520X-RAY DIFFRACTION100
3.06-3.20.30831330.25862558X-RAY DIFFRACTION100
3.2-3.360.30041150.25012571X-RAY DIFFRACTION99
3.36-3.570.28371520.2342526X-RAY DIFFRACTION99
3.57-3.850.28061350.2252531X-RAY DIFFRACTION99
3.85-4.240.27031320.21022544X-RAY DIFFRACTION99
4.24-4.850.23381530.19612542X-RAY DIFFRACTION98
4.85-6.110.28681490.21962556X-RAY DIFFRACTION98
6.11-70.340.27391290.23122631X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 28.4406 Å / Origin y: 9.8893 Å / Origin z: 37.1927 Å
111213212223313233
T0.336 Å20.0226 Å20.0066 Å2-0.3335 Å2-0.0006 Å2--0.4246 Å2
L0.0794 °20.0607 °20.1839 °2-0.0149 °20.1133 °2--0.8068 °2
S-0.0069 Å °-0.0041 Å °-0.0119 Å °0.0413 Å °-0.0152 Å °0.0295 Å °-0.0079 Å °-0.0264 Å °0.0129 Å °
Refinement TLS groupSelection details: all

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