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- PDB-1uar: Crystal structure of Rhodanese from Thermus thermophilus HB8 -

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Basic information

Entry
Database: PDB / ID: 1uar
TitleCrystal structure of Rhodanese from Thermus thermophilus HB8
ComponentsRhodanese
KeywordsTRANSFERASE / Rhodanese / Sulfurtransferase / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


thiosulfate sulfurtransferase activity
Similarity search - Function
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 ...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
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsSuzuki, Y. / Kakuta, Y. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be published
Title: Crystal structure of Rhodanese from Thermus thermophilus HB8
Authors: Suzuki, Y. / Kakuta, Y.
History
DepositionMar 17, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rhodanese
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3733
Polymers33,1891
Non-polymers1842
Water8,071448
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.200, 47.000, 86.200
Angle α, β, γ (deg.)90.00, 113.80, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Rhodanese /


Mass: 33188.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SJI0, thiosulfate sulfurtransferase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 448 / 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 Å3/Da / Density % sol: 38.05 % / Description: The file contains Friedel pairs.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 2000mme, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9792 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 65803 / Num. obs: 65803 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 19.5 Å2
Reflection shellResolution: 1.7→1.76 Å / % possible all: 21.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345data collection
SCALEPACKdata scaling
CNS1.1phasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→40.97 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 509566.48 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: The file contains Friedel pairs.
RfactorNum. reflection% reflectionSelection details
Rfree0.243 3104 5 %RANDOM
Rwork0.206 ---
obs0.206 62699 96.5 %-
all-65803 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.3838 Å2 / ksol: 0.363591 e/Å3
Displacement parametersBiso mean: 24.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20 Å2-0.85 Å2
2--5.9 Å20 Å2
3----5.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.7→40.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2259 0 12 448 2719
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.71
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.303 501 5.1 %
Rwork0.279 9297 -
obs--90.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CSS.PARAMWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMCSS.TOP
X-RAY DIFFRACTION4GOL.PARAMGOL.TOP

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