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- PDB-5evj: X-ray crystal structure of CrArsM, an arsenic (III) S-adenosylmet... -

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Basic information

Entry
Database: PDB / ID: 5evj
TitleX-ray crystal structure of CrArsM, an arsenic (III) S-adenosylmethionine methyltransferase from Chlamydomonas reinhardtii
ComponentsArsenite methyltransferase
KeywordsTRANSFERASE / METHYLTRANSFERASE / Arsenic Methyltransferase
Function / homology
Function and homology information


arsenite methyltransferase / methyltransferase activity / methylation
Similarity search - Function
Arsenite methyltransferase-like / 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 speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPackianathan, C. / Kandavelu, P. / Sankaran, B. / Rosen, B.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R37 GM55425 United States
CitationJournal: To Be Published
Title: Crystal structure of CrArsM, an arsenic (III) S-adenosylmethionine methyltransferase from Chlamydomonas reinhardtii
Authors: Packianathan, C. / Kandavelu, P. / Sankaran, B. / Rosen, B.P.
History
DepositionNov 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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 / 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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,2663
Polymers83,2432
Non-polymers231
Water4,414245
1
A: Arsenite methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6442
Polymers41,6211
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Arsenite methyltransferase


Theoretical massNumber of molelcules
Total (without water)41,6211
Polymers41,6211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)157.885, 157.885, 95.452
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Arsenite methyltransferase


Mass: 41621.465 Da / Num. of mol.: 2
Mutation: Y72W, C92A, C98A, C132A, C185A, C234A, C247A, C284A, C321A, W332Y, C352A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: arsM / Plasmid: PET28(a) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: K0BVM7
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 10% PEG 8000, 2.0 M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 34690 / Num. obs: 34690 / % possible obs: 100 % / Redundancy: 11.7 % / Biso Wilson estimate: 45.2 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 34.1
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 11.5 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 6.8 / % possible all: 100

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Processing

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

4fs8


Resolution: 2.4→45.58 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.914 / SU B: 5.341 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23048 1746 5 %RANDOM
Rwork0.18037 ---
obs0.18293 32914 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.03 Å2
Refinement stepCycle: 1 / Resolution: 2.4→45.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4667 0 1 245 4913
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0194774
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0321.9636481
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8065605
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.22423.628226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.02915751
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9821536
X-RAY DIFFRACTIONr_chiral_restr0.140.2704
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213722
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_it4.3384.1912426
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.5456.2623029
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.4124.4952348
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined10.72435.57367
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.227 130 -
Rwork0.17 2420 -
obs--98.61 %

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