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- PDB-8c9s: Catechol O-methyltransferase from Streptomyces avermitilis in com... -

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Basic information

Entry
Database: PDB / ID: 8c9s
TitleCatechol O-methyltransferase from Streptomyces avermitilis in complex with SAH
ComponentsPutative O-methyltransferase
KeywordsTRANSFERASE
Function / homology
Function and homology information


S-adenosylmethionine-dependent methyltransferase activity / O-methyltransferase activity / methylation / metal ion binding
Similarity search - Function
: / Class I-like SAM-dependent O-methyltransferase / O-methyltransferase / SAM-dependent O-methyltransferase class I-type profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
pyrrolidin-2-one / S-ADENOSYL-L-HOMOCYSTEINE / O-methyltransferase
Similarity search - Component
Biological speciesStreptomyces avermitilis MA-4680 = NBRC 14893 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsZhang, L. / Groves, M.R.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)893122European Union
CitationJournal: Chembiochem / Year: 2023
Title: Structural Characterization and Extended Substrate Scope Analysis of Two Mg 2+ -Dependent O-Methyltransferases from Bacteria.
Authors: Sokolova, N. / Zhang, L. / Deravi, S. / Oerlemans, R. / Groves, M.R. / Haslinger, K.
History
DepositionJan 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1May 10, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative O-methyltransferase
B: Putative O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4188
Polymers50,4312
Non-polymers9886
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-51 kcal/mol
Surface area16780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.398, 41.596, 104.207
Angle α, β, γ (deg.)90.000, 96.564, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative O-methyltransferase


Mass: 25215.326 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avermitilis MA-4680 = NBRC 14893 (bacteria)
Gene: SAVERM_5837 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q82B68
#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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-BAQ / pyrrolidin-2-one


Mass: 85.104 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C4H7NO
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.07 Å3/Da / Density % sol: 40.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2M Ammonium formate, 10% w/v Polyvinylpyrrolidone 20% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.8→46.09 Å / Num. obs: 36681 / % possible obs: 99.2 % / Redundancy: 7.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.158 / Net I/σ(I): 9.2
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 1.406 / Num. unique obs: 2144 / CC1/2: 0.603

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
Cootmodel building
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→46.09 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.162 / SU ML: 0.094 / Cross valid method: FREE R-VALUE / ESU R: 0.126 / ESU R Free: 0.125
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2107 1855 5.059 %
Rwork0.162 34814 -
all0.164 --
obs-36669 99.036 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 22.338 Å2
Baniso -1Baniso -2Baniso -3
1--1.127 Å20 Å2-0.492 Å2
2--0.571 Å20 Å2
3---0.652 Å2
Refinement stepCycle: LAST / Resolution: 1.8→46.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3388 0 66 173 3627
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133532
X-RAY DIFFRACTIONr_bond_other_d0.0010.0153388
X-RAY DIFFRACTIONr_angle_refined_deg1.5281.6414814
X-RAY DIFFRACTIONr_angle_other_deg1.3751.5827792
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8295448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.76121.17188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.53415556
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7191532
X-RAY DIFFRACTIONr_chiral_restr0.0730.2458
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024034
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02780
X-RAY DIFFRACTIONr_nbd_refined0.2010.2708
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.23146
X-RAY DIFFRACTIONr_nbtor_refined0.160.21732
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.21601
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2174
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1650.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2090.220
X-RAY DIFFRACTIONr_nbd_other0.2470.274
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1140.212
X-RAY DIFFRACTIONr_mcbond_it1.5612.1341792
X-RAY DIFFRACTIONr_mcbond_other1.5612.1341792
X-RAY DIFFRACTIONr_mcangle_it2.1543.1922234
X-RAY DIFFRACTIONr_mcangle_other2.1533.1922235
X-RAY DIFFRACTIONr_scbond_it2.7732.5151740
X-RAY DIFFRACTIONr_scbond_other2.7732.5151741
X-RAY DIFFRACTIONr_scangle_it4.2683.6332578
X-RAY DIFFRACTIONr_scangle_other4.2673.6322579
X-RAY DIFFRACTIONr_lrange_it5.09826.1913871
X-RAY DIFFRACTIONr_lrange_other5.0626.0563839
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8470.2981280.2632529X-RAY DIFFRACTION99.0679
1.847-1.8970.2531350.2352464X-RAY DIFFRACTION97.4503
1.897-1.9520.2641310.2082412X-RAY DIFFRACTION99.1423
1.952-2.0120.2391420.1962364X-RAY DIFFRACTION99.4444
2.012-2.0780.2311370.1772301X-RAY DIFFRACTION99.6322
2.078-2.1510.2091320.1642160X-RAY DIFFRACTION99.3068
2.151-2.2320.1911050.1582154X-RAY DIFFRACTION99.6032
2.232-2.3240.2461040.162110X-RAY DIFFRACTION99.64
2.324-2.4270.214940.1461992X-RAY DIFFRACTION99.5704
2.427-2.5450.205860.141869X-RAY DIFFRACTION98.9372
2.545-2.6830.214960.151763X-RAY DIFFRACTION96.9239
2.683-2.8450.222950.1561700X-RAY DIFFRACTION99.446
2.845-3.0420.213830.1611612X-RAY DIFFRACTION99.8821
3.042-3.2850.198780.1641522X-RAY DIFFRACTION99.0712
3.285-3.5980.2790.1511381X-RAY DIFFRACTION99.3873
3.598-4.0230.192640.1441250X-RAY DIFFRACTION99.095
4.023-4.6440.17550.1271125X-RAY DIFFRACTION99.2431
4.644-5.6840.213490.156920X-RAY DIFFRACTION96.4179
5.684-8.0270.209470.172745X-RAY DIFFRACTION100

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