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- PDB-9ko3: Crystal structure of Agrobacterium tumefaciens PmtA with SAH -

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Basic information

Entry
Database: PDB / ID: 9ko3
TitleCrystal structure of Agrobacterium tumefaciens PmtA with SAH
ComponentsMethyltransferase
KeywordsTRANSFERASE / Phospholipid N-mehyltransferase / Phosphatidylcholine
Function / homologyMethyltransferase domain 25 / Methyltransferase domain / methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / S-ADENOSYL-L-HOMOCYSTEINE / Methyltransferase
Function and homology information
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsWatanabe, Y.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)22K06096 Japan
Japan Society for the Promotion of Science (JSPS)20K15734 Japan
CitationJournal: To Be Published
Title: Crystal structure of Agrobacterium tumefaciens PmtA
Authors: Watanabe, Y.
History
DepositionNov 19, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methyltransferase
B: Methyltransferase
C: Methyltransferase
D: Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,8069
Polymers76,1734
Non-polymers1,6345
Water11,169620
1
A: Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4282
Polymers19,0431
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9060 Å2
MethodPISA
2
B: Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4282
Polymers19,0431
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8260 Å2
MethodPISA
3
C: Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4282
Polymers19,0431
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8130 Å2
MethodPISA
4
D: Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5243
Polymers19,0431
Non-polymers4802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-14 kcal/mol
Surface area8120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.942, 76.378, 87.185
Angle α, β, γ (deg.)90.00, 105.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Methyltransferase


Mass: 19043.137 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (strain C58) (bacteria)
Gene: Atu0300 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: A9CKE9
#2: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 620 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.94 Å3/Da / Density % sol: 58.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M lithium sulfate, 0.1M Tris-HCl pH 8.0, 25% polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 64020 / % possible obs: 99.5 % / Redundancy: 5.2 % / CC1/2: 0.979 / Rmerge(I) obs: 0.348 / Rrim(I) all: 0.387 / Net I/av σ(I): 6.81 / Net I/σ(I): 2.62
Reflection shellResolution: 1.95→2.07 Å / Redundancy: 5.3 % / Rmerge(I) obs: 2.105 / Mean I/σ(I) obs: 0.96 / Num. unique obs: 9367 / CC1/2: 0.454 / Rrim(I) all: 2.333 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260)refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→46.6 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2272 3123 4.89 %
Rwork0.1871 --
obs0.1891 63818 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→46.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5162 0 109 620 5891
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075420
X-RAY DIFFRACTIONf_angle_d0.8367406
X-RAY DIFFRACTIONf_dihedral_angle_d7.0053217
X-RAY DIFFRACTIONf_chiral_restr0.059851
X-RAY DIFFRACTIONf_plane_restr0.007939
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9547-1.98520.3331410.34062546X-RAY DIFFRACTION94
1.9852-2.01780.32961310.27882784X-RAY DIFFRACTION100
2.0178-2.05260.28171470.26742733X-RAY DIFFRACTION100
2.0526-2.08990.33061470.26412739X-RAY DIFFRACTION100
2.0899-2.13010.27251430.24452779X-RAY DIFFRACTION100
2.1301-2.17360.27411410.22972747X-RAY DIFFRACTION100
2.1736-2.22090.29131290.22622750X-RAY DIFFRACTION100
2.2209-2.27250.29591360.23522772X-RAY DIFFRACTION100
2.2725-2.32930.24491670.19782724X-RAY DIFFRACTION100
2.3293-2.39230.22971300.18962766X-RAY DIFFRACTION100
2.3923-2.46270.24161360.18512780X-RAY DIFFRACTION100
2.4627-2.54220.26961470.19892747X-RAY DIFFRACTION100
2.5422-2.6330.24871360.19682760X-RAY DIFFRACTION100
2.633-2.73850.25631320.19432780X-RAY DIFFRACTION100
2.7385-2.86310.24911440.18692750X-RAY DIFFRACTION100
2.8631-3.0140.24081510.18882762X-RAY DIFFRACTION100
3.014-3.20280.21141320.18552800X-RAY DIFFRACTION100
3.2028-3.450.22321320.17172773X-RAY DIFFRACTION100
3.45-3.79710.19111440.16292783X-RAY DIFFRACTION100
3.7971-4.34620.16341340.15042797X-RAY DIFFRACTION100
4.3462-5.47430.17991510.14232800X-RAY DIFFRACTION100
5.4743-46.60.19621720.17322823X-RAY DIFFRACTION100

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