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- PDB-2wdf: Termus thermophilus Sulfate thiohydrolase SoxB -

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Basic information

Entry
Database: PDB / ID: 2wdf
TitleTermus thermophilus Sulfate thiohydrolase SoxB
ComponentsSULFUR OXIDATION PROTEIN SOXB
KeywordsHYDROLASE / SULFUR-SULFUR HYDROLYSIS / SULFUR OXIDATION PATHWAY / SOX / SOXB / CYS S-THIOSULFONATE
Function / homology
Function and homology information


nucleotide catabolic process / outer membrane-bounded periplasmic space / hydrolase activity / nucleotide binding / metal ion binding
Similarity search - Function
Helix Hairpins - #570 / Thiosulfohydrolase SoxB / SoxB, N-terminal metallophosphatase domain / 5'-nucleotidase; domain 2 / 5'-Nucleotidase, C-terminal domain / 5'-Nucleotidase, C-terminal / 5'-nucleotidase, C-terminal domain / 5'-Nucleotidase/apyrase / 5'-Nucleotidase, C-terminal domain superfamily / Metallo-dependent phosphatases ...Helix Hairpins - #570 / Thiosulfohydrolase SoxB / SoxB, N-terminal metallophosphatase domain / 5'-nucleotidase; domain 2 / 5'-Nucleotidase, C-terminal domain / 5'-Nucleotidase, C-terminal / 5'-nucleotidase, C-terminal domain / 5'-Nucleotidase/apyrase / 5'-Nucleotidase, C-terminal domain superfamily / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Helix Hairpins / Metallo-dependent phosphatase-like / Helix non-globular / Special / 4-Layer Sandwich / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
: / TERTIARY-BUTYL ALCOHOL / Sulfur oxidation protein soxB
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsSauve, V. / Roversi, P. / Leath, K.J. / Garman, E.F. / Antrobus, R. / Lea, S.M. / Berks, B.C.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Mechanism for the Hydrolysis of a Sulfur-Sulfur Bond Based on the Crystal Structure of the Thiosulfohydrolase Soxb.
Authors: Sauve, V. / Roversi, P. / Leath, K.J. / Garman, E.F. / Antrobus, R. / Lea, S.M. / Berks, B.C.
History
DepositionMar 24, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Dec 13, 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SULFUR OXIDATION PROTEIN SOXB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9314
Polymers62,7471
Non-polymers1843
Water6,053336
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)70.363, 86.710, 95.133
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SULFUR OXIDATION PROTEIN SOXB / SOXB


Mass: 62747.434 Da / Num. of mol.: 1 / Fragment: RESIDUES 24-573
Source method: isolated from a genetically manipulated source
Details: THERMUS THERMOPHILUS HB27 SOXB / Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB27 / Plasmid: PVS048 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA 2 / Variant (production host): DE3 / References: UniProt: Q72IT0, EC: 3.12.2.1
#2: Chemical ChemComp-TBU / TERTIARY-BUTYL ALCOHOL / 2-METHYL-2-PROPANOL


Mass: 74.122 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsMANGANESE II ION (MN): SUPPLEMENTED AS 2 MM MNCL2
Sequence detailsSTREP II TAG AT THE N-TERMINUS REPLACED THE TAT SIGNAL PEPTIDE

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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: 2.42 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growDetails: 5 MM TRISHCL PH 8.0, 0.1M NACL, 12-13% T-BUTANOL, 0.05M TRIS-ACETAT PH 8.5, 1 MM MNCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418
DetectorType: BRUKER SMART 6000 / Detector: CCD / Details: MONTEL OPTICS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→64.1 Å / Num. obs: 32817 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 13 % / Biso Wilson estimate: 24.438 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 25.6
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 6.4 / % possible all: 99.4

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Processing

Software
NameVersionClassification
BUSTER-TNT2.5.1refinement
XPREPdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WDC

2wdc


Resolution: 2.08→64.15 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. AUTOBUSTER BETA 2.5.1 DECEMBER 2008. NATIVE STRUCTURE SUPPLEMENTED WITH MNCL2 TO ENSURE FULL OCCUPANCY OF THE MN IONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2284 1793 5.2 %RANDOM
Rwork0.1798 ---
obs0.1823 34616 97.66 %-
Displacement parametersBiso mean: 24.17 Å2
Baniso -1Baniso -2Baniso -3
1--0.73301299 Å20 Å20 Å2
2--2.79377574 Å20 Å2
3----2.06076275 Å2
Refinement stepCycle: LAST / Resolution: 2.08→64.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4296 0 7 336 4639
LS refinement shellResolution: 2.08→2.25 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2749 338 5.28 %
Rwork0.2182 6060 -
all0.2211 6398 -
obs--97.66 %

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