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

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Basic information

Entry
Database: PDB / ID: 2xva
TitleCrystal structure of the tellurite detoxification protein TehB from E. coli in complex with sinefungin
ComponentsTELLURITE RESISTANCE PROTEIN TEHB
KeywordsTRANSFERASE
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
SINEFUNGIN / Tellurite methyltransferase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 25, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2012Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Dec 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_conn / 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
C: TELLURITE RESISTANCE PROTEIN TEHB
D: TELLURITE RESISTANCE PROTEIN TEHB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,42111
Polymers90,6994
Non-polymers1,7227
Water13,727762
1
A: TELLURITE RESISTANCE PROTEIN TEHB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0562
Polymers22,6751
Non-polymers3811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TELLURITE RESISTANCE PROTEIN TEHB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1223
Polymers22,6751
Non-polymers4472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: TELLURITE RESISTANCE PROTEIN TEHB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1223
Polymers22,6751
Non-polymers4472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: TELLURITE RESISTANCE PROTEIN TEHB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1223
Polymers22,6751
Non-polymers4472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.100, 55.590, 129.700
Angle α, β, γ (deg.)90.00, 95.93, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.9999, 0.01324, 0.00262), (0.01259, 0.985, -0.172), (-0.004857, -0.1719, -0.9851)-49.54, -5.279, -68.05
2given(-0.4616, 0.2746, -0.8435), (0.2295, -0.8815, -0.4125), (-0.8569, -0.384, 0.3439)-28.47, -39.97, -66.83
3given(0.4546, 0.4, 0.7958), (-0.229, -0.811, 0.5384), (0.8608, -0.427, -0.2771)50.21, -19.57, -44.83

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Components

#1: Protein
TELLURITE RESISTANCE PROTEIN TEHB / TELLURITE METHYLTRANSFERASE


Mass: 22674.842 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 MG1655 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P25397
#2: Chemical
ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H23N7O5
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 762 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsSINEFUNGIN IS REPRESENTED AS ADENOSYL-ORNITHINE (SFG). WE OBSERVE SOME POSITIVE DENSITY NEAR THE ...SINEFUNGIN IS REPRESENTED AS ADENOSYL-ORNITHINE (SFG). WE OBSERVE SOME POSITIVE DENSITY NEAR THE SINEFUNGIN MOLECULE THAT WE CANNOT BUILD INTO. WE ONLY OBSERVE IT FOR THE SINEFUNGIN DATA AND NOT FROM THE S-ADENOSYL HOMOCYSTEINE. MOST LIKELY DUE TO A CONTAMINANT FROM THE SINEFUNGIN COMPOUND. ZN ION WAS BUILT IN SOME DENSITY WE COULD NOT ACCOUNT FOR. THE FLUORESCENT SCAN AT THE BEAMLINE REVEALED ZN AND THE ANOMALOUS MAP MATCHED THAT PEAK. WE DO NOT SEE THIS PEAK FOR THE S-ADENOSYL HOMOCYSTEINE DATA (PROBABLY DUE TO A CONTAMINANT FROM THE SINEFUNGIN COMPOUND).
Sequence detailsTHE I2V MUTATION WAS FROM CLONING TO THE HO SITE.

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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: 2.39 Å3/Da / Density % sol: 48.5 % / Description: NONE
Crystal growpH: 8 / Details: 0.2M NAF, 22% PEG 3350, 5MM SINEFUNGIN, pH 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 19, 2010 / Details: MIRRORS
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.9→42.1 Å / Num. obs: 62310 / % possible obs: 94.6 % / Observed criterion σ(I): 6 / Redundancy: 1.9 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.4
Reflection shellResolution: 1.9→2 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1.9 / % possible all: 97.2

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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: 1.9→40 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.911 / SU B: 7.621 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23423 3183 5.1 %RANDOM
Rwork0.17456 ---
obs0.17766 59055 93.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.607 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å2-0.02 Å2
2--0.38 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6271 0 111 762 7144
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0226634
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5151.9748999
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3545815
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.67823.631336
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.817151162
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6231560
X-RAY DIFFRACTIONr_chiral_restr0.1070.2993
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025060
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_it0.7761.53949
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.35126366
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.28832685
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5454.52614
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
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: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 237 -
Rwork0.24 4441 -
obs--96.87 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8138-0.4923-0.22661.12660.37440.46650.06680.0508-0.0153-0.022-0.10130.0229-0.0327-0.10430.03450.03720.0258-0.0060.0746-0.00730.0032-10.94-13.322-20.827
20.68280.3705-0.07250.5071-0.14650.5964-0.006-0.0155-0.08380.0247-0.0204-0.0601-0.079-0.00420.02640.05730.0042-0.00690.03490.00450.0158-39.115-15.674-45.031
31.0213-0.41540.39820.6055-0.17140.7770.03550.0117-0.0265-0.01210.0290.02160.0479-0.0076-0.06460.0554-0.0028-0.00910.01360.00140.0209-41.319-35.879-10.192
40.9340.498-0.03720.67910.07160.4244-0.036-0.0594-0.0599-0.0081-0.0038-0.0319-0.0022-0.03220.03980.0370.00680.00620.0444-0.00610.0172-8.618-39.194-51.845
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 197
2X-RAY DIFFRACTION2B-1 - 197
3X-RAY DIFFRACTION3C4 - 196
4X-RAY DIFFRACTION4D4 - 197

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