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- PDB-8t1a: Crystal Structure of S-adenosylmethionine-dependent methyltransfe... -

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Basic information

Entry
Database: PDB / ID: 8t1a
TitleCrystal Structure of S-adenosylmethionine-dependent methyltransferase UmaA from Mycobacterium tuberculosis (P32 Twin)
ComponentsS-adenosylmethionine-dependent methyltransferase UmaA
KeywordsTRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / UmaA
Function / homology
Function and homology information


cyclopropane-fatty-acyl-phospholipid synthase activity / lipid biosynthetic process / Transferases; Transferring one-carbon groups; Methyltransferases / 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 / S-adenosylmethionine-dependent methyltransferase UmaA
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700059C United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal Structure of S-adenosylmethionine-dependent methyltransferase UmaA from Mycobacterium tuberculosis (P32 Twin)
Authors: Lovell, S. / Seibold, S. / Battaile, K.P.
History
DepositionJun 2, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)68,6346
Polymers68,3252
Non-polymers3084
Water88349
1
A: S-adenosylmethionine-dependent methyltransferase UmaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3173
Polymers34,1631
Non-polymers1542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: S-adenosylmethionine-dependent methyltransferase UmaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3173
Polymers34,1631
Non-polymers1542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.665, 102.665, 50.525
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

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


Mass: 34162.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: umaA, Rv0469, LH57_02505 / Plasmid: MytuD.00149.b.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q6MX39, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 45.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: JCSG+ D6: 20% (w/v) PEG 4000, 0.1M HEPES pH 8.5, 0.2 M magnesium sulfate. MytuD.00149.b.B1.PW39156 at 26 mg/mL. Plate: 13026 well D6 drop 1. Puck: PSL-0501, Cryo: 20% Glycerol + 80% ...Details: JCSG+ D6: 20% (w/v) PEG 4000, 0.1M HEPES pH 8.5, 0.2 M magnesium sulfate. MytuD.00149.b.B1.PW39156 at 26 mg/mL. Plate: 13026 well D6 drop 1. Puck: PSL-0501, Cryo: 20% Glycerol + 80% Crystallant. Structure did not refine (high R-factors) in P3221 (-3m1). Refined in P32 (-3) with twin operator H, -H-K, -L.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Dec 10, 2022
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2→44.46 Å / Num. obs: 40241 / % possible obs: 100 % / Redundancy: 10 % / CC1/2: 0.996 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.041 / Rrim(I) all: 0.129 / Χ2: 0.99 / Net I/σ(I): 10.2 / Num. measured all: 403199
Reflection shellResolution: 2→2.05 Å / % possible obs: 100 % / Redundancy: 10.3 % / Rmerge(I) obs: 1.574 / Num. measured all: 30505 / Num. unique obs: 2964 / CC1/2: 0.438 / Rpim(I) all: 0.515 / Rrim(I) all: 1.657 / Χ2: 1.05 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_4933: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→44.46 Å / SU ML: 0 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 38.3 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2095 1915 4.76 %
Rwork0.172 --
obs0.1807 40222 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→44.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4326 0 20 49 4395
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024436
X-RAY DIFFRACTIONf_angle_d0.4435990
X-RAY DIFFRACTIONf_dihedral_angle_d12.5061596
X-RAY DIFFRACTIONf_chiral_restr0.037648
X-RAY DIFFRACTIONf_plane_restr0.003779
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.32251120.29032739X-RAY DIFFRACTION96
2.05-2.110.27221810.28742722X-RAY DIFFRACTION94
2.11-2.170.28221420.29042674X-RAY DIFFRACTION95
2.17-2.240.2632980.27012811X-RAY DIFFRACTION97
2.24-2.320.24251680.24872723X-RAY DIFFRACTION94
2.32-2.410.25981160.25272768X-RAY DIFFRACTION96
2.41-2.520.28611260.23632729X-RAY DIFFRACTION96
2.52-2.650.2721240.23412765X-RAY DIFFRACTION96
2.65-2.820.2061500.21952704X-RAY DIFFRACTION95
2.82-3.040.23361420.21392718X-RAY DIFFRACTION95
3.04-3.340.21111420.19782754X-RAY DIFFRACTION95
3.34-3.820.19271440.15962724X-RAY DIFFRACTION95
3.83-4.820.161440.11272735X-RAY DIFFRACTION95
4.82-44.460.22121260.1432741X-RAY DIFFRACTION95

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