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- PDB-5f2k: Crystal structure of mycobacterial fatty acid O-methyltransferase... -

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Basic information

Entry
Database: PDB / ID: 5f2k
TitleCrystal structure of mycobacterial fatty acid O-methyltransferase in complex with SAH and octanoate
Componentsfatty acid O-methyltransferase
KeywordsTRANSFERASE / fatty acid methyltransferase / octanoate / methyltransferase
Function / homology
Function and homology information


methyltransferase activity
Similarity search - Function
Methyltransferase, alpha-helical capping domain / Methyltransferase, alpha-helical capping domain / SAM dependent carboxyl methyltransferase / SAM dependent carboxyl methyltransferase / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich ...Methyltransferase, alpha-helical capping domain / Methyltransferase, alpha-helical capping domain / SAM dependent carboxyl methyltransferase / SAM dependent carboxyl methyltransferase / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
OCTANOIC ACID (CAPRYLIC ACID) / S-ADENOSYL-L-HOMOCYSTEINE / SAM dependent carboxyl methyltransferase
Similarity search - Component
Biological speciesMycobacterium marinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å
AuthorsPetronikolou, N. / Nair, S.K.
CitationJournal: Chem.Biol. / Year: 2015
Title: Biochemical Studies of Mycobacterial Fatty Acid Methyltransferase: A Catalyst for the Enzymatic Production of Biodiesel.
Authors: Petronikolou, N. / Nair, S.K.
History
DepositionDec 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: fatty acid O-methyltransferase
B: fatty acid O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,7306
Polymers80,6732
Non-polymers1,0574
Water14,448802
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-2 kcal/mol
Surface area28770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.074, 66.131, 98.086
Angle α, β, γ (deg.)90.00, 107.36, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein fatty acid O-methyltransferase


Mass: 40336.512 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium marinum (strain ATCC BAA-535 / M) (bacteria)
Strain: ATCC BAA-535 / M / Gene: MMAR_3356 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 / References: UniProt: B2HHT4
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-OCA / OCTANOIC ACID (CAPRYLIC ACID) / Caprylic acid


Mass: 144.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H16O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 802 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.18 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MgCl2, 0.1 M N-(2-acetamido)iminodiacetic acid [pH 6.5], 12% PEG 6000

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.978 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 101625 / % possible obs: 100 % / Redundancy: 4.2 % / Net I/σ(I): 20.5

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data scaling
PHENIXmodel building
ARPmodel building
Cootmodel building
PHENIXphasing
RefinementResolution: 1.6→25 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.935 / SU B: 1.665 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21838 4997 5 %RANDOM
Rwork0.19501 ---
obs0.19619 95148 98.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.239 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20.05 Å2
2---0.17 Å20 Å2
3---0.12 Å2
Refinement stepCycle: 1 / Resolution: 1.6→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5503 0 72 802 6377
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0195751
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0681.9627847
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7435723
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.38222.788269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.99815854
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7881558
X-RAY DIFFRACTIONr_chiral_restr0.0720.2861
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214510
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 308 -
Rwork0.256 5947 -
obs--84.05 %

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