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- PDB-7zkh: C-Methyltransferase PsmD from Streptomyces griseofuscus with boun... -

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Basic information

Entry
Database: PDB / ID: 7zkh
TitleC-Methyltransferase PsmD from Streptomyces griseofuscus with bound cofactor (crystal form 1)
ComponentsMethyltransferase
KeywordsTRANSFERASE / Rossmann fold / Cap domain / indole C3-methylation / S-adenosyl methionine
Function / homology
Function and homology information


biosynthetic process / methyltransferase activity / methylation
Similarity search - Function
Methyltransferase domain 25 / Methyltransferase domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / S-ADENOSYL-L-HOMOCYSTEINE / Unknown ligand / Methyltransferase
Similarity search - Component
Biological speciesStreptomyces griseofuscus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsWeiergraeber, O.H. / Amariei, D.A. / Pozhydaieva, N. / Pietruszka, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Catalysis / Year: 2022
Title: Enzymatic C3-Methylation of Indoles Using Methyltransferase PsmD-Crystal Structure, Catalytic Mechanism, and Preparative Applications
Authors: Amariei, D.A. / Pozhydaieva, N. / David, B. / Schneider, P. / Classen, T. / Gohlke, H. / Weiergraber, O.H. / Pietruszka, J.
History
DepositionApr 13, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3154
Polymers30,7801
Non-polymers5353
Water5,314295
1
A: Methyltransferase
hetero molecules

A: Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6298
Polymers61,5602
Non-polymers1,0696
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area2960 Å2
ΔGint5 kcal/mol
Surface area21970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.190, 95.990, 40.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-620-

HOH

21A-678-

HOH

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Components

#1: Protein Methyltransferase


Mass: 30780.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces griseofuscus (bacteria) / Gene: psmD / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: W8R3D8
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.03 Å3/Da / Density % sol: 39.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: PEG 1000, Tris-HCl

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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 PILATUS 6M-F / Detector: PIXEL / Date: Jun 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.4→53.36 Å / Num. obs: 49285 / % possible obs: 98.6 % / Redundancy: 8.2 % / Biso Wilson estimate: 21.39 Å2 / CC1/2: 1 / Rrim(I) all: 0.042 / Net I/σ(I): 22.73
Reflection shellResolution: 1.4→1.44 Å / Redundancy: 5.94 % / Mean I/σ(I) obs: 0.93 / Num. unique obs: 3292 / CC1/2: 0.402 / Rrim(I) all: 2.005 / % possible all: 89.7

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WZN

1wzn


Resolution: 1.4→53.36 Å / SU ML: 0.1567 / Cross valid method: FREE R-VALUE / Phase error: 19.5096
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.185 2465 5 %
Rwork0.1584 46819 -
obs0.1598 49284 98.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.52 Å2
Refinement stepCycle: LAST / Resolution: 1.4→53.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2060 0 24 295 2379
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00842428
X-RAY DIFFRACTIONf_angle_d0.98993340
X-RAY DIFFRACTIONf_chiral_restr0.0903352
X-RAY DIFFRACTIONf_plane_restr0.0084466
X-RAY DIFFRACTIONf_dihedral_angle_d13.1543872
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.430.29621210.27262291X-RAY DIFFRACTION87.71
1.43-1.460.28031310.25292491X-RAY DIFFRACTION95.69
1.46-1.490.29681350.21582567X-RAY DIFFRACTION98.61
1.49-1.520.28091340.19672548X-RAY DIFFRACTION98.49
1.52-1.560.23531370.18212598X-RAY DIFFRACTION99.13
1.56-1.60.23261350.17212574X-RAY DIFFRACTION98.76
1.6-1.650.22591370.17122603X-RAY DIFFRACTION99.31
1.65-1.70.18291350.1532563X-RAY DIFFRACTION99.34
1.7-1.760.20221390.13952625X-RAY DIFFRACTION99.39
1.76-1.830.18131360.12952602X-RAY DIFFRACTION99.53
1.83-1.920.1671370.13282598X-RAY DIFFRACTION99.53
1.92-2.020.17851390.13882629X-RAY DIFFRACTION99.68
2.02-2.150.18081380.13682636X-RAY DIFFRACTION99.78
2.15-2.310.15051390.13812625X-RAY DIFFRACTION99.6
2.31-2.540.18081400.15192673X-RAY DIFFRACTION99.82
2.54-2.910.19661400.16272663X-RAY DIFFRACTION99.72
2.91-3.670.17221420.15862699X-RAY DIFFRACTION99.68
3.67-53.360.17811500.16662834X-RAY DIFFRACTION99.67

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