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- PDB-7zgt: C-Methyltransferase PsmD from Streptomyces griseofuscus (apo form) -

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Basic information

Entry
Database: PDB / ID: 7zgt
TitleC-Methyltransferase PsmD from Streptomyces griseofuscus (apo form)
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
FORMIC ACID / : / PHOSPHATE ION / Methyltransferase
Similarity search - Component
Biological speciesStreptomyces griseofuscus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 4, 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
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methyltransferase
B: Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9307
Polymers61,5602
Non-polymers3705
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-16 kcal/mol
Surface area22010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.050, 87.490, 89.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Methyltransferase / C-Methyltransferase PsmD


Mass: 30780.125 Da / Num. of mol.: 2
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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.25 Å3/Da / Density % sol: 45.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: magnesium formate

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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 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.05→46.88 Å / Num. obs: 35369 / % possible obs: 99.6 % / Redundancy: 13.07 % / Biso Wilson estimate: 46.5 Å2 / CC1/2: 1 / Rrim(I) all: 0.117 / Net I/σ(I): 17.16
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 13.51 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 2572 / CC1/2: 0.354 / Rrim(I) all: 4.329 / % possible all: 99.3

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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: 2.05→46.88 Å / SU ML: 0.3649 / Cross valid method: FREE R-VALUE / Phase error: 33.7091
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2524 1766 5 %
Rwork0.2153 33552 -
obs0.2172 35318 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.51 Å2
Refinement stepCycle: LAST / Resolution: 2.05→46.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3903 0 19 155 4077
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00164155
X-RAY DIFFRACTIONf_angle_d0.41555691
X-RAY DIFFRACTIONf_chiral_restr0.0379615
X-RAY DIFFRACTIONf_plane_restr0.0029756
X-RAY DIFFRACTIONf_dihedral_angle_d10.56051437
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.110.39841340.36472535X-RAY DIFFRACTION99.22
2.11-2.170.37021330.33572538X-RAY DIFFRACTION99.48
2.17-2.240.39761310.36182518X-RAY DIFFRACTION98.37
2.24-2.320.48641320.38572508X-RAY DIFFRACTION97.67
2.32-2.410.32531340.28612528X-RAY DIFFRACTION99.55
2.41-2.520.31091360.2532585X-RAY DIFFRACTION99.74
2.52-2.650.28031350.24062570X-RAY DIFFRACTION99.74
2.65-2.820.31241360.23852576X-RAY DIFFRACTION99.93
2.82-3.040.29091350.232570X-RAY DIFFRACTION99.93
3.04-3.340.26171370.21722605X-RAY DIFFRACTION99.93
3.34-3.830.24781370.20362599X-RAY DIFFRACTION99.93
3.83-4.820.18311400.16852652X-RAY DIFFRACTION100
4.82-46.880.21081460.18432768X-RAY DIFFRACTION99.76
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)
11.911633039151.10862918869-2.184332370394.71199693304-0.8953645421122.913190542180.0268443013706-0.303106351645-0.5199798163890.384791797457-0.400173720411-1.027615911440.1613669592310.376311812860.3417634216290.464561982774-0.0336384727595-0.09894252476520.5437695386890.1261093854170.62281924290212.29364083099.1016549628935.3958837647
22.726610745541.12504238529-0.4610679613576.97764701948-0.953600708553.99317972324-0.1628163159940.333080569376-0.345008099725-0.450516005122-0.162010525342-0.628617442740.3281941891760.2304309733780.2954197965890.4863253535090.003799061917020.02000126448550.433092523505-0.004959745001860.3985652870382.872278041696.5546877039124.449011133
34.92892191033.024273040360.9498311069242.792858264430.5012523125862.666233207660.0917992685520.210624363716-0.463530730770.1271459306810.135865247165-0.3617403810090.1155409808910.452777974597-0.2233440896130.546491927044-0.03684290342890.0004921273119370.383493122618-0.06801430372490.48525267260516.118365654728.449637738825.3400163306
44.9874300043-1.116670234450.6089994179164.0362617981-0.752571835244.652795338270.0625208397457-0.0771632552943-0.04945035891020.350560023765-0.002746727320760.361582023461-0.0819750033077-0.319250086094-0.05770676754310.398736980422-0.06055544665720.03561451572420.3813472094560.02042751106480.334819214272-6.7051282912411.119832690230.3263497291
51.43623218669-0.04038105979560.9447258056676.67079385421.5646557723.373645372610.1097601762080.3213152779030.325416335819-0.41888569752-0.0827457992975-0.645381295528-0.3196517552560.251773997906-0.02851312799150.465305411658-0.03765968134050.01274780812190.4882138047550.08162728379570.48703129690521.982250923861.102711062233.5385949782
61.01722197229-0.7876736345760.1578443731894.427898647131.667600665233.35880663766-0.19471467726-0.001623823924520.1022045565090.1512719661670.161587768671-0.0690957332837-0.04823040355730.04101042691430.04197869256890.283837091808-0.0295710303144-0.04367513642040.3311870007850.05295095577550.33675824911718.997795408250.451842977341.6092612998
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 17 through 106 )AA17 - 1061 - 90
22chain 'A' and (resid 107 through 158 )AA107 - 15891 - 142
33chain 'A' and (resid 159 through 221 )AA159 - 221143 - 205
44chain 'A' and (resid 222 through 269 )AA222 - 269206 - 253
55chain 'B' and (resid 19 through 132 )BD19 - 1321 - 114
66chain 'B' and (resid 133 through 267 )BD133 - 267115 - 249

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