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- PDB-8hd2: Crystal structure of SAM dependent methyltransferase encoded in t... -

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Basic information

Entry
Database: PDB / ID: 8hd2
TitleCrystal structure of SAM dependent methyltransferase encoded in type II fatty acid biosynthesis gene cluster from ladderane lipid producing anammox bacteria
ComponentsMethyltransf_25 domain-containing protein
KeywordsBIOSYNTHETIC PROTEIN / anammox / fatty acid synthesis / ladderane lipid / SAM dependent methyltransferase
Function / homologyMethyltransferase domain 25 / Methyltransferase domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily / S-ADENOSYL-L-HOMOCYSTEINE / Methyltransferase domain-containing protein
Function and homology information
Biological speciesCandidatus Brocadia fulgida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsUegaki, T. / Nagano, S. / Hino, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)17H05444 Japan
Japan Society for the Promotion of Science (JSPS)19H04658 Japan
CitationJournal: Int J Mol Sci / Year: 2023
Title: Anammox Bacterial S -Adenosyl-l-Methionine Dependent Methyltransferase Crystal Structure and Its Interaction with Acyl Carrier Proteins.
Authors: Uegaki, T. / Takei, T. / Yamaguchi, S. / Fujiyama, K. / Sato, Y. / Hino, T. / Nagano, S.
History
DepositionNov 3, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methyltransf_25 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5922
Polymers41,2081
Non-polymers3841
Water4,918273
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14570 Å2
Unit cell
Length a, b, c (Å)35.016, 48.060, 49.828
Angle α, β, γ (deg.)82.590, 84.120, 70.670
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Methyltransf_25 domain-containing protein / AmxMT1


Mass: 41207.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Brocadia fulgida (bacteria) / Gene: KKO18993.1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: A0A0M2USF2
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.9 Å3/Da / Density % sol: 35.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 15 % PEG 2000, 0.1 M HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→45.12 Å / Num. obs: 38897 / % possible obs: 97.13 % / Redundancy: 3.4 % / Biso Wilson estimate: 18.86 Å2 / CC1/2: 0.994 / Net I/σ(I): 7
Reflection shellResolution: 1.6→1.63 Å / Num. unique obs: 1761 / CC1/2: 0.761

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
pointlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→45.12 Å / SU ML: 0.1522 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 21.1658
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2078 1881 4.84 %
Rwork0.1801 36975 -
obs0.1814 38856 97.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.64 Å2
Refinement stepCycle: LAST / Resolution: 1.6→45.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2571 0 26 273 2870
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00562667
X-RAY DIFFRACTIONf_angle_d0.85153604
X-RAY DIFFRACTIONf_chiral_restr0.0522378
X-RAY DIFFRACTIONf_plane_restr0.008460
X-RAY DIFFRACTIONf_dihedral_angle_d6.01350
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.23081350.21172759X-RAY DIFFRACTION95.1
1.64-1.690.27281510.21242767X-RAY DIFFRACTION95.67
1.69-1.750.22521310.212895X-RAY DIFFRACTION96.28
1.75-1.810.23731460.20112790X-RAY DIFFRACTION96.36
1.81-1.880.26111440.19352815X-RAY DIFFRACTION96.64
1.88-1.970.25671440.1912844X-RAY DIFFRACTION96.76
1.97-2.070.23171620.18482851X-RAY DIFFRACTION96.79
2.07-2.20.2251540.18292836X-RAY DIFFRACTION97.39
2.2-2.370.22571410.18482875X-RAY DIFFRACTION97.83
2.37-2.610.24991320.19312871X-RAY DIFFRACTION98.11
2.61-2.990.20921450.19222883X-RAY DIFFRACTION98.38
2.99-3.760.18651510.16552896X-RAY DIFFRACTION98.54
3.76-45.120.15681450.15872893X-RAY DIFFRACTION98.86

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