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- PDB-8bir: O-Methyltransferase Plu4895 in complex with SAH and AQ-256 -

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Basic information

Entry
Database: PDB / ID: 8bir
TitleO-Methyltransferase Plu4895 in complex with SAH and AQ-256
Componentsmethyltransferase Plu4895
KeywordsTRANSFERASE / methyltransferase / polyketide / anthraquinone
Function / homology
Function and homology information


O-methyltransferase activity / methylation
Similarity search - Function
O-methyltransferase domain / O-methyltransferase COMT-type / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
IODIDE ION / 1,3,8-tris(oxidanyl)anthracene-9,10-dione / S-ADENOSYL-L-HOMOCYSTEINE / Methyltransferase
Similarity search - Component
Biological speciesPhotorhabdus laumondii subsp. laumondii TTO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHuber, E.M. / Groll, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2023
Title: A set of closely related methyltransferases for site-specific tailoring of anthraquinone pigments.
Authors: Huber, E.M. / Kreling, L. / Heinrich, A.K. / Dunnebacke, M. / Pothig, A. / Bode, H.B. / Groll, M.
History
DepositionNov 2, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 17, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Nov 15, 2023Group: Data collection / Source and taxonomy / Category: chem_comp_atom / chem_comp_bond / entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.4Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: methyltransferase Plu4895
B: methyltransferase Plu4895
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,18620
Polymers76,8722
Non-polymers2,31418
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8610 Å2
ΔGint-124 kcal/mol
Surface area26000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.060, 40.130, 119.290
Angle α, β, γ (deg.)90.00, 92.47, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein methyltransferase Plu4895


Mass: 38435.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus laumondii subsp. laumondii TTO1 (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6L9JQS9

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Non-polymers , 6 types, 52 molecules

#2: Chemical ChemComp-SAH / 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-QOI / 1,3,8-tris(oxidanyl)anthracene-9,10-dione


Mass: 256.210 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H8O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: I
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.13 Å3/Da / Density % sol: 42.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M Ammonium iodide, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→46 Å / Num. obs: 25372 / % possible obs: 97.8 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 9.9
Reflection shellResolution: 2.4→2.5 Å / Rmerge(I) obs: 0.683 / Mean I/σ(I) obs: 2 / Num. unique obs: 2905 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8BIG

8big


Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.916 / SU B: 32.51 / SU ML: 0.354 / Cross valid method: THROUGHOUT / ESU R: 0.875 / ESU R Free: 0.347 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30113 1268 5 %RANDOM
Rwork0.26523 ---
obs0.26697 24089 97.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.207 Å2
Baniso -1Baniso -2Baniso -3
1--2.31 Å20 Å2-1.47 Å2
2--3.84 Å20 Å2
3----1.41 Å2
Refinement stepCycle: 1 / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5140 0 104 34 5278
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0135349
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174967
X-RAY DIFFRACTIONr_angle_refined_deg1.1821.6397235
X-RAY DIFFRACTIONr_angle_other_deg1.0661.58511553
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.975640
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.69424.106263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.9915971
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3411518
X-RAY DIFFRACTIONr_chiral_restr0.0390.2691
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025895
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021073
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_it0.7664.4162569
X-RAY DIFFRACTIONr_mcbond_other0.7664.4162569
X-RAY DIFFRACTIONr_mcangle_it1.4186.6223206
X-RAY DIFFRACTIONr_mcangle_other1.4186.6223207
X-RAY DIFFRACTIONr_scbond_it0.4154.4452780
X-RAY DIFFRACTIONr_scbond_other0.4154.4452779
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.8126.6424030
X-RAY DIFFRACTIONr_long_range_B_refined3.4450.0926130
X-RAY DIFFRACTIONr_long_range_B_other3.4450.096131
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.429 94 -
Rwork0.387 1778 -
obs--98.42 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5445-0.16451.1190.07240.02661.27590.0067-0.17520.0295-0.0212-0.00640.02650.001-0.104-0.00040.04640.0213-0.10120.3577-0.01370.273-18.66416.37722.2816
22.6148-0.04660.52690.0079-0.07781.4476-0.0619-0.24720.1006-0.01380.02010.01890.07890.1960.04180.06050.0277-0.1190.4754-0.04090.269315.418513.321636.8547
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 402
2X-RAY DIFFRACTION2B-1 - 402

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