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- PDB-8big: O-Methyltransferase Plu4895 in complex with SAH -

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Basic information

Entry
Database: PDB / ID: 8big
TitleO-Methyltransferase Plu4895 in complex with SAH
Componentsmethyltransferase Plu4895
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
NICKEL (II) ION / 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
B: methyltransferase Plu4895
C: methyltransferase Plu4895
D: methyltransferase Plu4895
E: methyltransferase Plu4895
F: methyltransferase Plu4895
G: methyltransferase Plu4895
H: methyltransferase Plu4895
hetero molecules


Theoretical massNumber of molelcules
Total (without water)294,14526
Polymers290,5808
Non-polymers3,56518
Water1,22568
1
A: methyltransferase Plu4895
hetero molecules

C: methyltransferase Plu4895
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5086
Polymers72,6452
Non-polymers8634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
Buried area6750 Å2
ΔGint-53 kcal/mol
Surface area25480 Å2
MethodPISA
2
B: methyltransferase Plu4895
E: methyltransferase Plu4895
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4735
Polymers72,6452
Non-polymers8283
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6580 Å2
ΔGint-40 kcal/mol
Surface area25840 Å2
MethodPISA
3
D: methyltransferase Plu4895
hetero molecules

H: methyltransferase Plu4895
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,6649
Polymers72,6452
Non-polymers1,0197
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area7140 Å2
ΔGint-59 kcal/mol
Surface area26200 Å2
MethodPISA
4
G: methyltransferase Plu4895
hetero molecules

F: methyltransferase Plu4895
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5006
Polymers72,6452
Non-polymers8554
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_544-x,y-1/2,-z-1/21
Buried area7010 Å2
ΔGint-48 kcal/mol
Surface area26180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.060, 95.900, 522.990
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
methyltransferase Plu4895


Mass: 36322.559 Da / Num. of mol.: 8
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, 86 molecules

#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-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.55 Å3/Da / Density % sol: 51.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.2 M MgCl2, 0.1 M MES pH 6.5, 10%PEG4000

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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: Jun 23, 2018
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: 70729 / % possible obs: 94.4 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 14.8
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.537 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 7149 / % possible all: 97.9

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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: 8BGT

8bgt


Resolution: 2.8→30 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.905 / SU B: 49.249 / SU ML: 0.415 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.464 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2877 3534 5 %RANDOM
Rwork0.2415 ---
obs0.2438 67135 94.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 227.76 Å2 / Biso mean: 82.312 Å2 / Biso min: 24.87 Å2
Baniso -1Baniso -2Baniso -3
1--1.66 Å20 Å2-0 Å2
2--4.25 Å2-0 Å2
3----2.59 Å2
Refinement stepCycle: final / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20432 0 224 68 20724
Biso mean--83.44 61.85 -
Num. residues----2542
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01321061
X-RAY DIFFRACTIONr_bond_other_d0.0010.01719716
X-RAY DIFFRACTIONr_angle_refined_deg1.1631.62828450
X-RAY DIFFRACTIONr_angle_other_deg1.0391.58245861
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.57252533
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.37624.0711039
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.152153861
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8811572
X-RAY DIFFRACTIONr_chiral_restr0.0360.22750
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0223174
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024206
X-RAY DIFFRACTIONr_rigid_bond_restr0.087340777
LS refinement shellResolution: 2.8→2.872 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 263 -
Rwork0.333 4987 -
all-5250 -
obs--97.95 %
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)
10.2511-0.1038-0.36130.23330.10541.3206-0.016-0.0325-0.01810.03640.00010.00230.02850.09070.01590.1552-0.01330.0020.1303-0.00090.163627.1262-4.5433-8.8227
20.07780.0877-0.04440.1762-0.32271.0459-0.01550.00010.0109-0.0288-0.0115-0.0080.044-0.03980.02710.16110.0010.00380.1381-0.01890.17152.1312-4.0858-47.3349
30.06510.10990.210.30590.23281.48940.06350.00870.00790.0132-0.03990.02130.15590.0572-0.02350.1730.0156-0.00630.1187-0.01260.1536-14.331535.0718-22.3995
40.61560.2046-0.26870.215-0.24750.8921-0.06440.07990.03510.03170.11860.0657-0.0046-0.0797-0.05430.1642-0.0224-0.00920.09840.00750.170926.5816-35.48-56.9925
50.2181-0.0673-0.21590.0539-0.09381.0380.01240.03050.03950.0023-0.0074-0.0076-0.1118-0.0177-0.0050.18780.0116-0.01610.11060.00620.166410.673620.5828-74.222
60.2557-0.09630.31440.3293-0.25881.69410.06450.03040.00770.0356-0.0808-0.10950.18290.0030.01620.24030.0298-0.00940.03520.00420.1747-14.809542.6192-121.5354
70.18880.00110.64641.03330.53562.6013-0.02490.10740.03410.09880.0648-0.17550.15630.3731-0.03990.1793-0.01630.02610.16520.02260.151235.11636.8459-110.7649
80.10490.0049-0.27310.1995-0.30951.1730.0049-0.0034-0.0115-0.05710.0034-0.00880.0542-0.0135-0.00830.1827-0.0307-0.01260.116-0.01870.1517-9.286-26.5731-85.7139
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 401
2X-RAY DIFFRACTION2B0 - 900
3X-RAY DIFFRACTION3C0 - 900
4X-RAY DIFFRACTION4D0 - 401
5X-RAY DIFFRACTION5E0 - 401
6X-RAY DIFFRACTION6F0 - 900
7X-RAY DIFFRACTION7G0 - 401
8X-RAY DIFFRACTION8H0 - 401

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