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- PDB-8bii: O-Methyltransferase Plu4895 (mutant H229N) in complex with SAH -

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Basic information

Entry
Database: PDB / ID: 8bii
TitleO-Methyltransferase Plu4895 (mutant H229N) in complex with SAH
Componentsmethyltransferase Plu4895 H229N mutant
KeywordsTRANSFERASE / methyltransferase / polyketide / anthraquinone
Function / homology
Function and homology information


O-methyltransferase activity / methylation
Similarity search - Function
O-methyltransferase domain / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / O-methyltransferase COMT-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Methyltransferase
Similarity search - Component
Biological speciesPhotorhabdus laumondii subsp. laumondii TTO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 H229N mutant
B: methyltransferase Plu4895 H229N mutant
C: methyltransferase Plu4895 H229N mutant
D: methyltransferase Plu4895 H229N mutant
E: methyltransferase Plu4895 H229N mutant
F: methyltransferase Plu4895 H229N mutant
G: methyltransferase Plu4895 H229N mutant
H: methyltransferase Plu4895 H229N mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)310,40517
Polymers307,2948
Non-polymers3,1119
Water93752
1
A: methyltransferase Plu4895 H229N mutant
B: methyltransferase Plu4895 H229N mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,5924
Polymers76,8242
Non-polymers7692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6580 Å2
ΔGint-42 kcal/mol
Surface area25870 Å2
MethodPISA
2
C: methyltransferase Plu4895 H229N mutant
H: methyltransferase Plu4895 H229N mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,5924
Polymers76,8242
Non-polymers7692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6560 Å2
ΔGint-42 kcal/mol
Surface area25180 Å2
MethodPISA
3
D: methyltransferase Plu4895 H229N mutant
hetero molecules

G: methyltransferase Plu4895 H229N mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,5924
Polymers76,8242
Non-polymers7692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area6640 Å2
ΔGint-39 kcal/mol
Surface area25570 Å2
MethodPISA
4
E: methyltransferase Plu4895 H229N mutant
F: methyltransferase Plu4895 H229N mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,6285
Polymers76,8242
Non-polymers8043
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6640 Å2
ΔGint-47 kcal/mol
Surface area25810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.920, 98.300, 531.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
methyltransferase Plu4895 H229N mutant


Mass: 38411.805 Da / Num. of mol.: 8 / Mutation: H229N
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
#2: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.5 Å3/Da / Density % sol: 50.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Sodium citrate, 0.1 M bis-tris propane pH 7.5, 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: Oct 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→49 Å / Num. obs: 76974 / % possible obs: 99.4 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 12.1
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.592 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 7541

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8BIG

8big


Resolution: 2.8→30 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.905 / SU B: 46.471 / SU ML: 0.394 / Cross valid method: THROUGHOUT / ESU R Free: 0.428 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28129 3845 5 %RANDOM
Rwork0.23505 ---
obs0.23734 73065 98.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 73.643 Å2
Baniso -1Baniso -2Baniso -3
1--3.56 Å2-0 Å20 Å2
2--2.37 Å2-0 Å2
3---1.19 Å2
Refinement stepCycle: 1 / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20366 0 209 52 20627
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01320998
X-RAY DIFFRACTIONr_bond_other_d0.0010.01620079
X-RAY DIFFRACTIONr_angle_refined_deg1.1471.62828369
X-RAY DIFFRACTIONr_angle_other_deg1.0311.58646367
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.68352529
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.5724.1371037
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.189153856
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8131572
X-RAY DIFFRACTIONr_chiral_restr0.0340.22745
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0223464
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024600
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_it0.7175.14610167
X-RAY DIFFRACTIONr_mcbond_other0.7175.14610167
X-RAY DIFFRACTIONr_mcangle_it1.347.71812679
X-RAY DIFFRACTIONr_mcangle_other1.347.71812680
X-RAY DIFFRACTIONr_scbond_it0.3575.12810831
X-RAY DIFFRACTIONr_scbond_other0.3575.12810831
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.7377.67315691
X-RAY DIFFRACTIONr_long_range_B_refined2.49558.07322760
X-RAY DIFFRACTIONr_long_range_B_other2.49458.07322760
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 274 -
Rwork0.336 5204 -
obs--99.42 %
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)
10.4505-0.099-0.35570.30170.30541.60350.0149-0.16930.1141-0.037-0.0858-0.0114-0.02170.05840.0710.2337-0.0554-0.03110.4183-0.0520.1825-9.1893-26.6316121.6029
20.62580.0073-0.61210.25830.39271.9453-0.1701-0.0173-0.30590.0234-0.0022-0.0431-0.02870.08560.17230.1761-0.01190.02760.33680.01690.31572.94-46.308891.7776
30.6432-0.2511-0.53980.20120.12462.59550.0585-0.15790.0788-0.1505-0.01690.00050.1096-0.1021-0.04170.3122-0.06210.02440.2719-0.0520.2185-22.8641-52.736953.7009
40.42620.0038-0.55730.2090.21981.81510.0395-0.01030.01020.0072-0.05350.13140.0011-0.05090.0140.4682-0.05420.00850.0543-0.03240.317712.808-78.222138.2569
50.23260.07110.57520.80170.10851.6994-0.08560.01570.0148-0.0650.0861-0.0064-0.02280.2193-0.00040.2209-0.04010.05350.4934-0.0730.140123.5583-99.4638106.7637
60.16820.12940.27220.5288-0.09862.1053-0.0377-0.09930.0853-0.3390.10610.20370.00760.0924-0.06840.4814-0.1172-0.03330.24450.00960.19922.5007-103.296775.2983
70.2347-0.1846-0.58210.77160.48741.5732-0.0512-0.0745-0.0294-0.12630.0013-0.06520.14260.11580.04990.5120.0091-0.03840.06510.05060.2887-22.7494-92.663712.5617
80.45190.1814-0.1780.2275-0.6352.36210.0255-0.03030.0974-0.0449-0.00630.0065-0.1694-0.0084-0.01910.60030.00070.08970.0024-0.01240.2276-15.9123-35.438721.0372
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 900
2X-RAY DIFFRACTION2B0 - 900
3X-RAY DIFFRACTION3C0 - 900
4X-RAY DIFFRACTION4D0 - 900
5X-RAY DIFFRACTION5E0 - 401
6X-RAY DIFFRACTION6F0 - 900
7X-RAY DIFFRACTION7G0 - 900
8X-RAY DIFFRACTION8H0 - 900

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