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- PDB-2xvm: Crystal structure of the tellurite detoxification protein TehB fr... -

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Basic information

Entry
Database: PDB / ID: 2xvm
TitleCrystal structure of the tellurite detoxification protein TehB from E. coli in complex with SAH
ComponentsTELLURITE RESISTANCE PROTEIN TEHB
KeywordsTRANSFERASE / ANTIBIOTIC RESISTANCE
Function / homology
Function and homology information


tellurite methyltransferase / response to tellurium ion / S-adenosylmethionine-dependent methyltransferase activity / methyltransferase activity / response to toxic substance / methylation / response to antibiotic / cytosol
Similarity search - Function
Tellurite resistance methyltransferase, TehB / Tellurite resistance methyltransferase TehB-like domain / Tellurite resistance protein TehB / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Tellurite methyltransferase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsChoudhury, H.G. / Cameron, A.D. / Iwata, S. / Beis, K.
CitationJournal: Biochem.J. / Year: 2011
Title: Structure and Mechanism of the Chalcogen Detoxifying Protein Tehb from Escherichia Coli.
Authors: Choudhury, H.G. / Cameron, A.D. / Iwata, S. / Beis, K.
History
DepositionOct 26, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: TELLURITE RESISTANCE PROTEIN TEHB
B: TELLURITE RESISTANCE PROTEIN TEHB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1194
Polymers45,3502
Non-polymers7692
Water9,224512
1
A: TELLURITE RESISTANCE PROTEIN TEHB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0592
Polymers22,6751
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TELLURITE RESISTANCE PROTEIN TEHB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0592
Polymers22,6751
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)130.362, 55.644, 59.420
Angle α, β, γ (deg.)90.00, 97.72, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.5454, -0.4511, 0.7064), (0.454, -0.8675, -0.2034), (0.7045, 0.2098, 0.6779)
Vector: -30.9, -13.34, 26)

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Components

#1: Protein TELLURITE RESISTANCE PROTEIN TEHB / TELLURITE METHYLTRANSFERASE


Mass: 22674.842 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: MG1655 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P25397
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 512 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ILE 2 TO VAL ENGINEERED RESIDUE IN CHAIN B, ILE 2 TO VAL

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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: 2.14 Å3/Da / Density % sol: 42.44 % / Description: NONE
Crystal growpH: 8 / Details: 0.2M NAF, 22% PEG3350, 1MM SAM, pH 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 7, 2010 / Details: MIRRORS
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.48→28.2 Å / Num. obs: 69781 / % possible obs: 98.9 % / Observed criterion σ(I): 6 / Redundancy: 5.3 % / Biso Wilson estimate: 19.9 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.1
Reflection shellResolution: 1.48→1.56 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.7 / % possible all: 96.2

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Processing

Software
NameVersionClassification
REFMAC5.5.0106refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2I6G

2i6g


Resolution: 1.48→28.26 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.809 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22976 3456 5 %RANDOM
Rwork0.17029 ---
obs0.17337 66104 98.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.87 Å2
Baniso -1Baniso -2Baniso -3
1--1.32 Å2-0 Å2-0.06 Å2
2--2.55 Å2-0 Å2
3----1.25 Å2
Refinement stepCycle: LAST / Resolution: 1.48→28.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3146 0 52 512 3710
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0223379
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9121.9724594
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5775426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.0923.663172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.84815603
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0291531
X-RAY DIFFRACTIONr_chiral_restr0.1330.2506
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022587
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_it2.1671.52006
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.20923247
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.1131373
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.9334.51329
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.59333379
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.479→1.517 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 204 -
Rwork0.257 4711 -
obs--95.4 %

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