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

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Basic information

Entry
Database: PDB / ID: 7zkg
TitleC-Methyltransferase PsmD from Streptomyces griseofuscus with bound cofactor (crystal form 2)
ComponentsMethyltransferase
KeywordsTRANSFERASE / Rossmann fold / Cap domain / indole C3-methylation / S-adenosyl methionine
Function / homologyMethyltransferase domain 25 / Methyltransferase domain / biosynthetic process / methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / PHOSPHATE ION / S-ADENOSYL-L-HOMOCYSTEINE / Methyltransferase
Function and homology information
Biological speciesStreptomyces griseofuscus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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

Downloads & links

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Assembly

Deposited unit
A: Methyltransferase
B: Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,37214
Polymers61,5602
Non-polymers1,81112
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-74 kcal/mol
Surface area21620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.710, 138.710, 162.060
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11A-451-

HOH

21A-454-

HOH

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Components

#1: Protein Methyltransferase


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.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 3.61 Å3/Da / Density % sol: 65.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: SOKALAN CP 42, 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 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.3→56.32 Å / Num. obs: 41427 / % possible obs: 100 % / Redundancy: 39.29 % / Biso Wilson estimate: 61.18 Å2 / CC1/2: 1 / Rrim(I) all: 0.122 / Net I/σ(I): 28.55
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 40.66 % / Mean I/σ(I) obs: 1.07 / Num. unique obs: 3019 / CC1/2: 0.54 / Rrim(I) all: 4.586 / % possible all: 100

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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: 2.3→56.32 Å / SU ML: 0.3018 / Cross valid method: FREE R-VALUE / Phase error: 24.4999
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2159 2072 5 %
Rwork0.1886 39336 -
obs0.1899 41408 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 76.49 Å2
Refinement stepCycle: LAST / Resolution: 2.3→56.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3949 0 62 86 4097
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024174
X-RAY DIFFRACTIONf_angle_d0.48145715
X-RAY DIFFRACTIONf_chiral_restr0.0374620
X-RAY DIFFRACTIONf_plane_restr0.0037768
X-RAY DIFFRACTIONf_dihedral_angle_d12.4281447
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.350.32621360.33052580X-RAY DIFFRACTION99.74
2.35-2.410.31621350.28642556X-RAY DIFFRACTION100
2.41-2.480.32721370.2772600X-RAY DIFFRACTION100
2.48-2.550.32951340.26882556X-RAY DIFFRACTION99.96
2.55-2.630.35351360.28852585X-RAY DIFFRACTION100
2.63-2.730.25581360.25772587X-RAY DIFFRACTION100
2.73-2.840.29551370.23312590X-RAY DIFFRACTION99.96
2.84-2.970.27921370.20822600X-RAY DIFFRACTION99.96
2.97-3.120.2351360.20592593X-RAY DIFFRACTION99.96
3.12-3.320.24111380.22192608X-RAY DIFFRACTION99.96
3.32-3.570.2141380.18452631X-RAY DIFFRACTION100
3.57-3.930.19481390.16672632X-RAY DIFFRACTION100
3.93-4.50.18161390.15542651X-RAY DIFFRACTION100
4.5-5.670.16461430.15542705X-RAY DIFFRACTION100
5.67-56.320.20411510.17742862X-RAY DIFFRACTION99.7
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)
11.12496893139-1.59864097033-0.0717919182966.34284064251-3.534195635543.0858030690.09170236177840.071800146813-0.107613322025-0.192853935453-0.23868158346-0.5719946088250.9413653490510.6021481308130.1017915478570.53999622802-0.0393310331442-0.004269752908240.469029736928-0.01067947723460.53824741088114.558897473753.931162109854.1044751776
24.11991756513-1.168290912530.382595825472.953949762930.2280810549312.12639466649-0.009541761837920.067996489080.0223844364151-0.1098804712190.0370705394812-0.1281007227350.01589253950570.159171328512-0.02747785156290.413630136848-0.0628621608847-0.003481579032270.4047197952820.007533857360940.39911039291316.61232710168.427310787952.1740897568
31.4265744387-0.5948390557930.9752549651572.87395584078-1.902027653434.43086576961-0.0158095985655-0.021827082413-0.0894571748213-0.05241781403670.01029801047270.1453603396510.305446113433-0.49640375215-0.04127751772440.430945553487-0.09322050133340.01803972228560.4666322816150.002204347783330.5146092915936.1383956334558.77304215863.3268546443
44.483542170963.33083547097-4.317264274165.26837270281-2.717437946565.43647861475-0.0920117499371-1.58942211075-0.6449361287840.241475562334-0.3902915492-0.385336357578-0.382935398930.7568655593630.4566893933480.5065322510520.123639325799-0.02022426850740.8536496385270.2217196616460.6624991837481.9436757424432.284306170996.1709668337
53.954052065710.735631448461-1.445335719232.68894075299-3.194878715714.47168121799-0.560160773868-1.35653120868-0.9961207732620.0811375101929-0.735578238206-1.081770999510.6169155197491.340538306251.218103446810.8929153325730.179381652030.1553133915131.870098339430.8011981688871.250235674311.070489785523.978808203798.8789302681
64.962374214010.683207305412-2.036087595653.55937860159-0.5954666702042.45470447386-0.839133419381-0.0903053644695-1.14690978184-0.2916142364050.1223880734680.09009944762490.295600443697-0.04081954070040.470064416120.6748939454860.07183626570190.1062642865050.4104623658570.06324338878480.6396147168652.0279903950827.801215821783.2194851084
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 14 through 52 )AA14 - 521 - 39
22chain 'A' and (resid 53 through 158 )AA53 - 15840 - 145
33chain 'A' and (resid 159 through 267 )AA159 - 267146 - 254
44chain 'B' and (resid 17 through 76 )BI17 - 761 - 60
55chain 'B' and (resid 77 through 118 )BI77 - 11861 - 102
66chain 'B' and (resid 119 through 266 )BI119 - 266103 - 250

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