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- PDB-7lxi: Crystal structure of S-adenosylmethionine-dependent methyltransfe... -

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Basic information

Entry
Database: PDB / ID: 7lxi
TitleCrystal structure of S-adenosylmethionine-dependent methyltransferase UmaA from Mycobacterium tuberculosis in complex with SAH
ComponentsS-adenosylmethionine-dependent methyltransferase UmaA
KeywordsTRANSFERASE / SSGCID / S-adenosylmethionine-dependent methyltransferase / SAM-dependent methyltransferase / UmaA / Mycobacterium tuberculosis / short-chain fatty acid modification / SAH / S-Adenosyl-l-homocysteine / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


lipid biosynthetic process / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / methylation / plasma membrane / cytoplasm
Similarity search - Function
: / Mycolic acid cyclopropane synthase / Mycolic acid cyclopropane synthetase / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
NITRATE ION / PHOSPHATE ION / S-ADENOSYL-L-HOMOCYSTEINE / S-adenosylmethionine-dependent methyltransferase UmaA
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of S-adenosylmethionine-dependent methyltransferase UmaA from Mycobacterium tuberculosis in complex with SAH
Authors: Sroge, C.D. / Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionMar 3, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: S-adenosylmethionine-dependent methyltransferase UmaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1468
Polymers34,1631
Non-polymers9837
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-9 kcal/mol
Surface area12900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.220, 103.220, 49.150
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-548-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein S-adenosylmethionine-dependent methyltransferase UmaA / SAM-dependent methyltransferase UmaA


Mass: 34162.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: umaA, Rv0469, LH57_02505 / Plasmid: MytuD.00149.b.B1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q6MX39, Transferases; Transferring one-carbon groups; Methyltransferases

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Non-polymers , 7 types, 193 molecules

#2: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: 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
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.22 Å3/Da / Density % sol: 44.51 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Microlytics MCSG1 screen, condition C9: 32% w/V PEG4000, 800 mM lithium chloride, 100 mM Tris base/HCl, pH 8.50: MytuD.00149.b.B1.PW38903, tray 318922c9, crystal soaked for 6 hours in ...Details: Microlytics MCSG1 screen, condition C9: 32% w/V PEG4000, 800 mM lithium chloride, 100 mM Tris base/HCl, pH 8.50: MytuD.00149.b.B1.PW38903, tray 318922c9, crystal soaked for 6 hours in reservoir with 5 mM SAH, cryoprotectant: 20% ethylene glycol + soak buffer, puck xeo4-1.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jan 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 22257 / % possible obs: 99.9 % / Redundancy: 9.368 % / Biso Wilson estimate: 36.706 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.053 / Rrim(I) all: 0.056 / Χ2: 0.923 / Net I/σ(I): 26.41
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.95-25.4170.6312.6316410.8290.699100
2-2.066.4390.4514.1915760.9120.49199.9
2.06-2.127.1880.3785.315410.9470.40899.8
2.12-2.187.8880.2877.6614860.9680.307100
2.18-2.258.4140.2359.6814620.9840.25100
2.25-2.339.0390.211.8714210.9890.21299.9
2.33-2.4210.3270.1714.5513470.9920.17999.8
2.42-2.5210.8750.14517.2313150.9950.15299.9
2.52-2.6310.8680.12120.1512480.9970.12799.9
2.63-2.7610.8910.09325.4212160.9980.09899.8
2.76-2.9110.9270.07928.2411460.9980.08399.9
2.91-3.0810.9440.06334.0810970.9990.06699.9
3.08-3.310.990.04943.0710150.9990.051100
3.3-3.5610.9540.03855.89700.9990.039100
3.56-3.910.8250.03264.8487210.033100
3.9-4.3610.8130.02969.6380410.031100
4.36-5.0310.7180.02772.3571710.028100
5.03-6.1710.6770.0366.0161910.031100
6.17-8.7210.5730.02768.3147810.02999.8
8.72-509.4550.02178.9228610.02398.3

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.19refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 7L9U

7l9u


Resolution: 1.95→43.07 Å / SU ML: 0.1725 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.9903
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1961 2062 9.27 %0
Rwork0.1654 20178 --
obs0.1683 22240 99.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.99 Å2
Refinement stepCycle: LAST / Resolution: 1.95→43.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2241 0 37 186 2464
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00662337
X-RAY DIFFRACTIONf_angle_d0.73283155
X-RAY DIFFRACTIONf_chiral_restr0.0455342
X-RAY DIFFRACTIONf_plane_restr0.006418
X-RAY DIFFRACTIONf_dihedral_angle_d13.8572854
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-20.25671090.22831353X-RAY DIFFRACTION100
2-2.050.25311400.19331334X-RAY DIFFRACTION100
2.05-2.10.25431610.19111297X-RAY DIFFRACTION99.93
2.1-2.160.22921450.17861323X-RAY DIFFRACTION99.86
2.16-2.230.21861320.17881353X-RAY DIFFRACTION100
2.23-2.310.21211600.17951290X-RAY DIFFRACTION99.86
2.31-2.40.23681410.17831322X-RAY DIFFRACTION99.93
2.4-2.510.27431280.17521347X-RAY DIFFRACTION99.8
2.51-2.650.21071240.18131361X-RAY DIFFRACTION99.87
2.65-2.810.21951390.17941317X-RAY DIFFRACTION99.79
2.81-3.030.20681040.18581403X-RAY DIFFRACTION99.93
3.03-3.330.21751450.17181335X-RAY DIFFRACTION100
3.33-3.820.16171340.13811367X-RAY DIFFRACTION100
3.82-4.80.14191510.13391347X-RAY DIFFRACTION100
4.81-43.070.18911490.16651429X-RAY DIFFRACTION99.94
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)
17.052280454373.710044635490.7000370216032.93761228106-1.004119559731.997259727490.3651847797120.1241768454980.330400965344-0.158942244273-0.21282586924-1.118657904-0.6177073858220.987181097285-0.02145572852470.376283714695-0.1496885188890.1422348431770.538803372192-0.08812291311690.72465761628849.353295297513.86958964399.15843408856
21.87554445006-0.5384368495140.4017862698512.221491890480.3267614829372.66471596597-0.0009461447843470.2416318775290.135234605749-0.210597585221-0.0230523868785-0.158762037077-0.04286810524440.1546983172040.002600337905330.167456768536-0.04645067209210.03110197131570.1893873379950.0139011699450.16428663232727.850648355812.8150256087-4.33271838125
32.105537327340.291815463252.172379199921.2859542727-0.1406827252253.79368104097-0.2175845576360.1233785229210.552341595863-0.002615752413340.00280707296879-0.189119024896-0.5581490937770.1748812734270.2182101488890.33957767296-0.04234817386520.01192895612870.2308244774120.01619306225370.46699158583529.373682504832.64042632884.53691543371
41.4648920438-0.934862832610.5821155821993.45658532564-1.470013386262.01863992596-0.142263889516-0.1884503728710.2172828011560.5046390526760.0198791758385-0.434246235109-0.2072939697860.08126517156520.1437003408180.259961395646-0.0472983254194-0.01480588721440.217940825855-0.05182452194090.24532391471533.708361212818.482196000614.1947522938
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 4 through 24 )4 - 241 - 21
22chain 'A' and (resid 25 through 170 )25 - 17022 - 167
33chain 'A' and (resid 171 through 227 )171 - 227168 - 220
44chain 'A' and (resid 228 through 286 )228 - 286221 - 279

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