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- PDB-1urh: The "Rhodanese" fold and catalytic mechanism of 3-mercaptopyruvat... -

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Basic information

Entry
Database: PDB / ID: 1urh
TitleThe "Rhodanese" fold and catalytic mechanism of 3-mercaptopyruvate sulfotransferases: Crystal structure of SseA from Escherichia coli
Components3-MERCAPTOPYRUVATE SULFURTRANSFERASE
KeywordsTRANSFERASE / SULFUR-TRANSFERASE / RHODANESE
Function / homology
Function and homology information


3-mercaptopyruvate sulfurtransferase / 3-mercaptopyruvate sulfurtransferase activity / thiosulfate-cyanide sulfurtransferase activity / DNA protection / response to oxidative stress / response to antibiotic / cytosol
Similarity search - Function
Sulfurtransferase TST/MPST-like / Rhodanese signature 1. / Rhodanese C-terminal signature. / Thiosulphate sulfurtransferase, conserved site / Rhodanese-like domain / Oxidized Rhodanese; domain 1 / Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily ...Sulfurtransferase TST/MPST-like / Rhodanese signature 1. / Rhodanese C-terminal signature. / Thiosulphate sulfurtransferase, conserved site / Rhodanese-like domain / Oxidized Rhodanese; domain 1 / Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
SULFITE ION / 3-mercaptopyruvate sulfurtransferase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSpallarossa, A. / Forlani, F. / Carpen, A. / Armirotti, A. / Pagani, S. / Bolognesi, M. / Bordo, D.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: The "Rhodanese" Fold and Catalytic Mechanism of 3-Mercaptopyruvate Sulfurtransferases: Crystal Structure of Ssea from Escherichia Coli
Authors: Spallarossa, A. / Forlani, F. / Carpen, A. / Armirotti, A. / Pagani, S. / Bolognesi, M. / Bordo, D.
History
DepositionOct 30, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2003Provider: 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 / struct_conn
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.pdbx_leaving_atom_flag
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-MERCAPTOPYRUVATE SULFURTRANSFERASE
B: 3-MERCAPTOPYRUVATE SULFURTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5633
Polymers61,4832
Non-polymers801
Water1,22568
1
A: 3-MERCAPTOPYRUVATE SULFURTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)30,7421
Polymers30,7421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: 3-MERCAPTOPYRUVATE SULFURTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8222
Polymers30,7421
Non-polymers801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)150.170, 150.170, 37.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein 3-MERCAPTOPYRUVATE SULFURTRANSFERASE / SSEA / RHODANESE-LIKE PROTEIN / MST


Mass: 30741.596 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: RESIDUES A186-A189 AND B181-B191 ARE NOT INCLUDED IN THE MODEL.
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PEN1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P31142, 3-mercaptopyruvate sulfurtransferase
#2: Chemical ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O
Compound details3-MERCAPTOPYRUVATE + CYANIDE = PYRUVATE + THIOCYANATE.
Has protein modificationY

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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: 3.5 Å3/Da / Density % sol: 65 %
Crystal growpH: 6.5 / Details: pH 6.50
Crystal grow
*PLUS
Temperature: 294 K / pH: 8 / Method: vapor diffusion, hanging drop / Details: Spallarossa, A., (2003) Acta Cryst., D59, 168.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
114 mg/mlprotein1drop
250 mMTris-HCl1droppH8.0
350 mM1dropNaCl
41.9 Mammonium sulfate1reservoir
540 mMMES1reservoirpH6.2
62 %(v/v)PEG4001reservoir
710 mM1reservoirMnCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393
DetectorDate: Jul 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. obs: 21524 / % possible obs: 96 % / Observed criterion σ(I): 2 / Redundancy: 14 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 16
Reflection shellResolution: 2.8→2.85 Å / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 2 / % possible all: 97.9
Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 40 Å / % possible obs: 95.6 % / Num. measured all: 312079 / Rmerge(I) obs: 0.066
Reflection shell
*PLUS
% possible obs: 97.9 % / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 2.2

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RHS

1rhs


Resolution: 2.8→40 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.289 --RANDOM
Rwork0.234 ---
obs0.234 21546 100 %-
Refinement stepCycle: LAST / Resolution: 2.8→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4010 0 4 68 4082
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 2.9 Å / Rfactor Rfree: 0.447 / Rfactor Rwork: 0.385

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