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- PDB-2wdd: Termus thermophilus Sulfate thiohydrolase SoxB in complex with Sulfate -

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Basic information

Entry
Database: PDB / ID: 2wdd
TitleTermus thermophilus Sulfate thiohydrolase SoxB in complex with Sulfate
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
ACETATE ION / : / TERTIARY-BUTYL ALCOHOL / Sulfur oxidation protein soxB
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 1.3Dec 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

Downloads & links

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Assembly

Deposited unit
A: SULFUR OXIDATION PROTEIN SOXB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2358
Polymers62,7471
Non-polymers4877
Water10,665592
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.834, 86.618, 96.095
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 599 molecules

#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-TBU / TERTIARY-BUTYL ALCOHOL / 2-METHYL-2-PROPANOL


Mass: 74.122 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MN / MANGANESE (II) ION


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


Mass: 18.015 Da / Num. of mol.: 592 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsMANGANESE II ION (MN): SUPPLEMENTED AS 2 MM DIAMMONIUM SULFATE SULFATE ION (SO4): SUPPLEMENTED AS 2 ...MANGANESE II ION (MN): SUPPLEMENTED AS 2 MM DIAMMONIUM SULFATE SULFATE ION (SO4): SUPPLEMENTED AS 2 MM DIAMMONIUM SULFATE
Sequence detailsSTREP II TAG AT THE NTERMINUS 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, 0.05M TRIS-ACETATE PH 8.5, 12-13% T-BUTANOL, 1 MM MNCL2 AND 1MM NH42SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.943
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.943 Å / Relative weight: 1
ReflectionResolution: 1.5→39.5 Å / Num. obs: 86525 / % possible obs: 95.8 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 16.38 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.7
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 3 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 3.3 / % possible all: 87.1

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Processing

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

2wdc


Resolution: 1.5→39.5 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. AUTOBUSTER BETA VERSION 2.5.1 DECEMBER 2008. SULFATE IS A PRODUCT OF THE REACTION CATALYSED BY THIS ENZYME.
RfactorNum. reflection% reflectionSelection details
Rfree0.196 4584 5 %RANDOM
Rwork0.17 ---
obs0.171 91109 95.6 %-
Displacement parametersBiso mean: 19.13 Å2
Baniso -1Baniso -2Baniso -3
1-0.70134 Å20 Å20 Å2
2---0.36387 Å20 Å2
3----0.33746 Å2
Refinement stepCycle: LAST / Resolution: 1.5→39.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4290 0 26 592 4908
LS refinement shellResolution: 1.5→1.59 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2112 684 5.16 %
Rwork0.1908 12582 -
all0.1918 13266 -
obs--95.61 %

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