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- PDB-8xt7: The crystal structure of human AS3MT -

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Basic information

Entry
Database: PDB / ID: 8xt7
TitleThe crystal structure of human AS3MT
ComponentsArsenite methyltransferase
KeywordsTRANSFERASE / Arsenic methyltransferase / S-denosylmethionine-dependent methyltransferase activity.
Function / homology
Function and homology information


arsenite methyltransferase / arsonoacetate metabolic process / arsenite methyltransferase activity / toxin metabolic process / Methylation / methylation / cytosol
Similarity search - Function
Arsenite methyltransferase-like / Methyltransferase domain / Methyltransferase domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Arsenite methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsChun, I.S. / Kim, M.S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: To Be Published
Title: The crystal structure of human AS3MT
Authors: Chun, I.S. / Kim, M.S.
History
DepositionJan 10, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 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: Arsenite methyltransferase
B: Arsenite methyltransferase
C: Arsenite methyltransferase
D: Arsenite methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,4818
Polymers144,2334
Non-polymers2484
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.829, 85.772, 97.852
Angle α, β, γ (deg.)90.00, 104.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Arsenite methyltransferase / Methylarsonite methyltransferase / S-adenosyl-L-methionine:arsenic(III) methyltransferase


Mass: 36058.188 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AS3MT, CYT19 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HBK9, arsenite methyltransferase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.42 Å3/Da / Density % sol: 49.14 %
Crystal growTemperature: 296.15 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Sodium Malonate pH7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.59→47.38 Å / Num. obs: 40586 / % possible obs: 94.38 % / Redundancy: 3 % / CC1/2: 0.978 / Net I/σ(I): 9.185
Reflection shellResolution: 2.59→2.683 Å / Mean I/σ(I) obs: 1.611 / Num. unique obs: 3849 / CC1/2: 0.704

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→46.86 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2279 1999 4.93 %
Rwork0.2012 --
obs0.2025 40584 93.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.59→46.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9534 0 16 123 9673
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0119746
X-RAY DIFFRACTIONf_angle_d1.13713162
X-RAY DIFFRACTIONf_dihedral_angle_d17.1293592
X-RAY DIFFRACTIONf_chiral_restr0.0631458
X-RAY DIFFRACTIONf_plane_restr0.0081690
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.650.35941210.32092351X-RAY DIFFRACTION81
2.65-2.720.33411480.30552847X-RAY DIFFRACTION98
2.72-2.80.32641480.29892835X-RAY DIFFRACTION97
2.8-2.890.28791490.2522884X-RAY DIFFRACTION98
2.89-30.29831440.24422792X-RAY DIFFRACTION97
3-3.120.26781470.22822818X-RAY DIFFRACTION97
3.12-3.260.2681450.22092819X-RAY DIFFRACTION96
3.26-3.430.30141460.22932803X-RAY DIFFRACTION95
3.43-3.640.24611450.19662781X-RAY DIFFRACTION96
3.64-3.930.20621420.16882753X-RAY DIFFRACTION93
3.93-4.320.17561380.16022667X-RAY DIFFRACTION91
4.32-4.950.15211330.15642586X-RAY DIFFRACTION88
4.95-6.230.21491450.19072770X-RAY DIFFRACTION94
6.23-46.860.20351480.1952879X-RAY DIFFRACTION95

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