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- PDB-1yt8: Crystal Structure of Thiosulfate sulfurtransferase from Pseudomon... -

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Basic information

Entry
Database: PDB / ID: 1yt8
TitleCrystal Structure of Thiosulfate sulfurtransferase from Pseudomonas aeruginosa
Componentsthiosulfate sulfurtransferaseRhodanese
KeywordsTRANSFERASE / thiosulfate sulfurtransferase / Rhodanase domains / Cyanide detoxification / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


thiosulfate sulfurtransferase activity
Similarity search - Function
Rhodanese signature 1. / 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 / Probable thiosulfate sulfurtransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsKumaran, D. / Swaminathan, S. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal Structure of Thiosulfate sulfurtransferase from Pseudomonas aeruginosa
Authors: Kumaran, D. / Swaminathan, S.
History
DepositionFeb 10, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / struct_conn ...audit_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag ..._audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE The electron density for the side chain of residue 84 supports a His rather than a Leu and ...SEQUENCE The electron density for the side chain of residue 84 supports a His rather than a Leu and modeled accordingly.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: thiosulfate sulfurtransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1413
Polymers58,9691
Non-polymers1722
Water9,440524
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.348, 114.476, 69.438
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein thiosulfate sulfurtransferase / Rhodanese


Mass: 58969.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I0N4, thiosulfate sulfurtransferase
#2: Chemical ChemComp-SO3 / SULFITE ION / Sulfite


Mass: 80.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 524 / Source method: isolated from a natural source / Formula: H2O

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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: 2.7 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 8000, Ammonium sulfate, Sodium cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.979, 0.976, 0.94
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 17, 2004 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.9761
30.941
ReflectionResolution: 1.9→50 Å / Num. all: 56427 / Num. obs: 56427 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Biso Wilson estimate: 13.6 Å2

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data scaling
SOLVEphasing
SHARPphasing
ARP/wARPmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.9→48.04 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 470811.16 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.209 1667 3 %RANDOM
Rwork0.185 ---
obs0.185 55493 98.7 %-
all-55493 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.2361 Å2 / ksol: 0.337289 e/Å3
Displacement parametersBiso mean: 19.4 Å2
Baniso -1Baniso -2Baniso -3
1--3.8 Å20 Å20 Å2
2--6.38 Å20 Å2
3----2.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.9→48.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4030 0 10 524 4564
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d0.8
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.262 240 2.7 %
Rwork0.208 8589 -
obs--95.6 %

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