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- PDB-6cx6: The structure of an As(III) S-adenosylmethionine methyltransferas... -

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Basic information

Entry
Database: PDB / ID: 6cx6
TitleThe structure of an As(III) S-adenosylmethionine methyltransferase with As(III) and S-adenosyl-L-homocysteine (SAH)
ComponentsArsenic methyltransferase
KeywordsTRANSFERASE / methyltransferase
Function / homology
Function and homology information


arsenite methyltransferase / methyltransferase activity / methylation / metal ion binding
Similarity search - Function
Ribosomal Protein L9; domain 1 - #100 / Arsenite methyltransferase-like / Ribosomal Protein L9; domain 1 / Methyltransferase domain / Methyltransferase domain / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ARSENIC / S-ADENOSYL-L-HOMOCYSTEINE / Arsenite methyltransferase
Similarity search - Component
Biological speciesCyanidioschyzon sp. 5508 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsPackianathan, C. / Kandavelu, P. / Rosen, B.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM55425 United States
CitationJournal: Biochemistry / Year: 2018
Title: The Structure of an As(III) S-Adenosylmethionine Methyltransferase with 3-Coordinately Bound As(III) Depicts the First Step in Catalysis.
Authors: Packianathan, C. / Kandavelu, P. / Rosen, B.P.
History
DepositionApr 2, 2018Deposition site: RCSB / Processing site: RCSB
SupersessionJun 27, 2018ID: 5JWN
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.2Aug 1, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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: Arsenic methyltransferase
B: Arsenic methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,5196
Polymers83,6002
Non-polymers9194
Water84747
1
A: Arsenic methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2603
Polymers41,8001
Non-polymers4592
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Arsenic methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2603
Polymers41,8001
Non-polymers4592
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.797, 101.797, 175.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number93
Space group name H-MP4222
Components on special symmetry positions
IDModelComponents
11B-519-

HOH

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Components

#1: Protein Arsenic methyltransferase


Mass: 41800.176 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyanidioschyzon sp. 5508 (eukaryote) / Gene: arsM / Plasmid: pET28(a) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C0JV69, arsenite methyltransferase
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-ARS / ARSENIC


Mass: 74.922 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: As
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O

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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: 2.71 Å3/Da / Density % sol: 54.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.4 M potassium phosphate dibasic, 0.4 M sodium phosphate monobasic, 0.1 M imidazole, pH 8.0, 0.2 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 18, 2013 / Details: Mirror
RadiationMonochromator: double crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.84→100 Å / Num. obs: 22216 / % possible obs: 99.4 % / Redundancy: 18.7 % / Biso Wilson estimate: 50.2 Å2 / Rpim(I) all: 0.028 / Rsym value: 0.119 / Net I/σ(I): 22
Reflection shellResolution: 2.84→2.94 Å / Redundancy: 15.2 % / Mean I/σ(I) obs: 2.8 / Num. unique obs: 2058 / Rpim(I) all: 0.16 / Rsym value: 0.69 / % possible all: 95.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4FS8

4fs8


Resolution: 2.84→48.87 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.873 / SU B: 17.346 / SU ML: 0.327 / Cross valid method: THROUGHOUT / ESU R: 5.09 / ESU R Free: 0.421 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29122 1128 5.1 %RANDOM
Rwork0.21505 ---
obs0.21878 21179 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 62.888 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å2-0 Å20 Å2
2--0.03 Å2-0 Å2
3----0.06 Å2
Refinement stepCycle: 1 / Resolution: 2.84→48.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5174 0 54 47 5275
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195332
X-RAY DIFFRACTIONr_bond_other_d0.0010.025030
X-RAY DIFFRACTIONr_angle_refined_deg1.6541.9777216
X-RAY DIFFRACTIONr_angle_other_deg0.866311557
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2815661
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.2523.465254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.17115883
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2571544
X-RAY DIFFRACTIONr_chiral_restr0.0910.2801
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026065
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021247
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.1156.1532656
X-RAY DIFFRACTIONr_mcbond_other4.1166.1532655
X-RAY DIFFRACTIONr_mcangle_it6.4459.2183313
X-RAY DIFFRACTIONr_mcangle_other6.4449.2183314
X-RAY DIFFRACTIONr_scbond_it3.9726.492672
X-RAY DIFFRACTIONr_scbond_other3.9736.492672
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.5129.5943903
X-RAY DIFFRACTIONr_long_range_B_refined9.81649.5546201
X-RAY DIFFRACTIONr_long_range_B_other9.81549.5566202
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.84→2.913 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 84 -
Rwork0.313 1441 -
obs--93.85 %

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