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- PDB-4fs8: The structure of an As(III) S-adenosylmethionine methyltransferas... -

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Basic information

Entry
Database: PDB / ID: 4fs8
TitleThe structure of an As(III) S-adenosylmethionine methyltransferase: insights into the mechanism of arsenic biotransformation
ComponentsArsenic methyltransferase
KeywordsTRANSFERASE / Rossmann Fold / Arsenic 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
Arsenite methyltransferase
Similarity search - Component
Biological speciesCyanidioschyzon sp. 5508 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsAjees, A.A. / Marapakala, K. / Packianathan, C. / Sankaran, B. / Rosen, B.P.
Citation
Journal: Biochemistry / Year: 2012
Title: Structure of an As(III) S-Adenosylmethionine Methyltransferase: Insights into the Mechanism of Arsenic Biotransformation.
Authors: Ajees, A.A. / Marapakala, K. / Packianathan, C. / Sankaran, B. / Rosen, B.P.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Crystallization and preliminary X-ray crystallographic analysis of the ArsM arsenic(III) S-adenosylmethionine methyltransferase.
Authors: Marapakala, K. / Ajees, A.A. / Qin, J. / Sankaran, B. / Rosen, B.P.
History
DepositionJun 27, 2012Deposition site: RCSB / Processing site: RCSB
SupersessionJul 11, 2012ID: 3P7E
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Arsenic methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3532
Polymers42,3131
Non-polymers401
Water5,459303
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.750, 47.198, 101.677
Angle α, β, γ (deg.)90.00, 115.67, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Arsenic methyltransferase


Mass: 42312.734 Da / Num. of mol.: 1 / Fragment: UNP residues 1-370
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyanidioschyzon sp. 5508 (eukaryote) / Strain: 5508 / Gene: arsM / Plasmid: pET28-asrM7B / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: C0JV69
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.17 Å3/Da / Density % sol: 43.21 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7
Details: 18% polyethylene glycol 3350, 0.2 M calcium acetate and 0.1 M Tris-HCl pH 7.0, EVAPORATION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 5, 2010
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. all: 34951 / Num. obs: 33151 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.034
Reflection shell
Resolution (Å)Redundancy (%)Diffraction-ID
1.78-1.843.51
1.84-1.9241
1.92-24.51
2-2.114.61
2.11-2.2244.61

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.225 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20493 1756 5 %RANDOM
Rwork0.17694 ---
obs0.17843 33151 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.398 Å2
Baniso -1Baniso -2Baniso -3
1--1.57 Å20 Å2-0.92 Å2
2--2.35 Å2-0 Å2
3----1.57 Å2
Refinement stepCycle: LAST / Resolution: 1.78→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2535 0 1 303 2839
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192606
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4971.9653528
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9175328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.81123.615130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.79515440
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4181522
X-RAY DIFFRACTIONr_chiral_restr0.1070.2387
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212014
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.78-1.8250.2551140.2262293345099.5
1.84-1.923466100
1.92-23483100
2-2.113492100
2.11-2.243463100
2.24-2.423507100
2.42-2.663471100
2.66-3.043527100
3.04-3.833509100
3.83-50358399.1

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