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- PDB-2wdc: Termus thermophilus Sulfate thiohydrolase SoxB in complex with gl... -

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Basic information

Entry
Database: PDB / ID: 2wdc
TitleTermus thermophilus Sulfate thiohydrolase SoxB in complex with glycerol
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 / SAD / 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 1.1Aug 19, 2015Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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)63,99918
Polymers62,7471
Non-polymers1,25117
Water10,160564
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)71.345, 86.456, 95.974
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, 581 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-TBU / TERTIARY-BUTYL ALCOHOL / 2-METHYL-2-PROPANOL


Mass: 74.122 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O
#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.: 564 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsMANGANESE II ION (MN): CARRIED THROUGH PURIFICATION GLYCEROL (GOL): FROM CRYOPROTECTANT SOLUTION ...MANGANESE II ION (MN): CARRIED THROUGH PURIFICATION GLYCEROL (GOL): FROM CRYOPROTECTANT SOLUTION TERTIARY-BUTYL ALCOHOL (TBU): FROM XTALLISATION MOTHER LIQUOR ACETATE ION (ACT): FROM XTALLISATION MOTHER LIQUOR
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 TRISHC PH 8.0, 0.1 M NACL, 0.05 M TRIS-ACETATE PH 8.5, 12-13% T-BUTANOL

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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: 1.5→57.3 Å / Num. obs: 90719 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 9.8 % / Biso Wilson estimate: 15.59 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 26
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 1.6 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER-TNT2.5.1refinement
XPREPdata reduction
SCALAdata scaling
SHELXDphasing
SHARPphasing
SOLOMONphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.5→57.26 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. GLYCEROL MOLECULES FROM CRYOPROTECTANT. PHASED WITH MN AND S ANOMALOUS SIGNAL.
RfactorNum. reflection% reflectionSelection details
Rfree0.193 4808 5 %RANDOM
Rwork0.165 ---
obs0.167 95526 99.8 %-
Displacement parametersBiso mean: 17.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.47331 Å20 Å20 Å2
2---0.07928 Å20 Å2
3---0.55259 Å2
Refinement stepCycle: LAST / Resolution: 1.5→57.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4282 0 78 564 4924
LS refinement shellResolution: 1.5→1.59 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2049 756 4.99 %
Rwork0.1918 14409 -
all0.1924 15165 -
obs--99.84 %

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