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- PDB-9ko5: Crystal structure of Agrobacterium tumefaciens PmtA with 5'-methy... -

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Entry
Database: PDB / ID: 9ko5
TitleCrystal structure of Agrobacterium tumefaciens PmtA with 5'-methylthioadenosine
ComponentsMethyltransferase
KeywordsTRANSFERASE / Phospholipid N-mehyltransferase / Phosphatidylcholine
Function / homologyMethyltransferase domain 25 / Methyltransferase domain / methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / 5'-DEOXY-5'-METHYLTHIOADENOSINE / Methyltransferase
Function and homology information
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)77,3628
Polymers76,1734
Non-polymers1,1894
Water8,989499
1
A: Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3402
Polymers19,0431
Non-polymers2971
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3402
Polymers19,0431
Non-polymers2971
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3402
Polymers19,0431
Non-polymers2971
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3402
Polymers19,0431
Non-polymers2971
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.611, 76.394, 87.227
Angle α, β, γ (deg.)90.00, 105.56, 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-MTA / 5'-DEOXY-5'-METHYLTHIOADENOSINE


Mass: 297.334 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H15N5O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 499 / 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: 2.93 Å3/Da / Density % sol: 58.07 %
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: 2.04→50 Å / Num. obs: 64020 / % possible obs: 99.3 % / Redundancy: 5.3 % / CC1/2: 0.984 / Rmerge(I) obs: 0.322 / Rrim(I) all: 0.358 / Net I/σ(I): 7.1
Reflection shellResolution: 2.04→2.16 Å / Rmerge(I) obs: 2.055 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 8449 / CC1/2: 0.409 / Rrim(I) all: 2.275

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260)refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.04→46.7 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2091 2733 4.89 %
Rwork0.1703 --
obs0.1722 55903 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.04→46.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5145 0 80 499 5724
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075375
X-RAY DIFFRACTIONf_angle_d0.8287347
X-RAY DIFFRACTIONf_dihedral_angle_d6.3373192
X-RAY DIFFRACTIONf_chiral_restr0.058846
X-RAY DIFFRACTIONf_plane_restr0.007932
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0402-2.07540.3081420.26892555X-RAY DIFFRACTION96
2.0754-2.11310.29891320.24862653X-RAY DIFFRACTION99
2.1131-2.15380.25381280.22572614X-RAY DIFFRACTION99
2.1538-2.19780.28021350.21782643X-RAY DIFFRACTION99
2.1978-2.24550.25571300.2132652X-RAY DIFFRACTION99
2.2455-2.29780.28121410.21282645X-RAY DIFFRACTION100
2.2978-2.35520.21721420.18392637X-RAY DIFFRACTION99
2.3552-2.41890.22721370.18282635X-RAY DIFFRACTION99
2.4189-2.49010.24981240.18042653X-RAY DIFFRACTION100
2.4901-2.57050.23351550.18372655X-RAY DIFFRACTION100
2.5705-2.66230.22141170.18072674X-RAY DIFFRACTION100
2.6623-2.76890.21971330.18452639X-RAY DIFFRACTION100
2.7689-2.89490.21571430.1812675X-RAY DIFFRACTION100
2.8949-3.04750.20831380.18182677X-RAY DIFFRACTION100
3.0475-3.23840.22751290.18332674X-RAY DIFFRACTION100
3.2384-3.48840.23781280.17052686X-RAY DIFFRACTION100
3.4884-3.83930.19741440.1512682X-RAY DIFFRACTION100
3.8393-4.39440.13841250.13392693X-RAY DIFFRACTION100
4.3944-5.53510.1731440.12932694X-RAY DIFFRACTION100
5.5351-46.6760.17831660.15162734X-RAY DIFFRACTION100

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