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- PDB-5eg5: As (III) S-adenosylmethyltransferase cysteine mutant C72A bound P... -

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Basic information

Entry
Database: PDB / ID: 5eg5
TitleAs (III) S-adenosylmethyltransferase cysteine mutant C72A bound Phenylarsine oxide (PhAs(III) in the arsenic binding site
ComponentsArsenic methyltransferase
KeywordsTRANSFERASE / 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
Phenylarsine oxide / Arsenite methyltransferase
Similarity search - Component
Biological speciesCyanidioschyzon sp. 5508 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsPackianathan, C. / Marapakala, K. / Kandavelu, P. / Rosen, B.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R37GM55425 United States
CitationJournal: To Be Published
Title: As (III) S-adenosylmethyltransferase cysteine mutant C72A bound Phenylarsine oxide (PhAs(III) in the arsenic binding site
Authors: Packianathan, C. / Marapakala, K. / Kandavelu, P. / Rosen, B.P.
History
DepositionOct 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Arsenic methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9763
Polymers41,7681
Non-polymers2082
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.255, 47.369, 100.261
Angle α, β, γ (deg.)90.00, 113.59, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Arsenic methyltransferase


Mass: 41768.109 Da / Num. of mol.: 1 / Mutation: C72A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyanidioschyzon sp. 5508 (eukaryote) / Gene: arsM / Plasmid: PET28(a) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C0JV69
#2: Chemical ChemComp-PA0 / Phenylarsine oxide / oxo(phenyl)arsane


Mass: 168.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5AsO
#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 18% PEG 3350, 0.2M Ca(OAC)2, 0.1M Tris pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 31, 2013
RadiationMonochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.97→27.31 Å / Num. obs: 23330 / % possible obs: 89.6 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 29.8
Reflection shellResolution: 1.972→2.043 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 9.06 / % possible all: 96.9

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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: 4FS8

4fs8


Resolution: 1.97→27.31 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.907 / SU B: 4.822 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25016 1192 5.1 %RANDOM
Rwork0.19548 ---
obs0.19826 22159 89.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.313 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0.01 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.97→27.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2530 0 8 183 2721
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192598
X-RAY DIFFRACTIONr_bond_other_d0.0010.022462
X-RAY DIFFRACTIONr_angle_refined_deg1.8431.9683512
X-RAY DIFFRACTIONr_angle_other_deg1.05535655
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.9585323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.14423.359128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.1215438
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7571523
X-RAY DIFFRACTIONr_chiral_restr0.1050.2385
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022970
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02621
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_it2.8743.2661289
X-RAY DIFFRACTIONr_mcbond_other2.873.2621288
X-RAY DIFFRACTIONr_mcangle_it4.0034.8861610
X-RAY DIFFRACTIONr_mcangle_other4.0024.891611
X-RAY DIFFRACTIONr_scbond_it3.8223.7061308
X-RAY DIFFRACTIONr_scbond_other3.8213.7071309
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6845.3971902
X-RAY DIFFRACTIONr_long_range_B_refined7.61927.0313087
X-RAY DIFFRACTIONr_long_range_B_other7.61827.0373088
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.972→2.023 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 96 -
Rwork0.216 1700 -
obs--94.63 %

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