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- PDB-1e0c: SULFURTRANSFERASE FROM AZOTOBACTER VINELANDII -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1e0c
TitleSULFURTRANSFERASE FROM AZOTOBACTER VINELANDII
ComponentsSULFURTRANSFERASE
KeywordsSULFURTRANSFERASE / SULFUR METABOLISM / THIOSULFATE:CYANIDE SULFURTRANSFERASE
Function / homology
Function and homology information


thiosulfate sulfurtransferase / thiosulfate sulfurtransferase activity / cytoplasm
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 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
Thiosulfate sulfurtransferase
Similarity search - Component
Biological speciesAZOTOBACTER VINELANDII (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.8 Å
AuthorsBordo, D. / Deriu, D. / Colnaghi, R. / Carpen, A. / Pagani, S. / Bolognesi, M.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: The Crystal Structure of a Sulfurtransferase from Azotobacter Vinelandii Highlights the Evolutionary Relationship between the Rhodanese and Phosphatase Enzyme Families
Authors: Bordo, D. / Deriu, D. / Colnaghi, R. / Carpen, A. / Pagani, S. / Bolognesi, M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Crystallization and Preliminary Crystallographic Investigations of Rhodanese from Azotobacter Vinelandii
Authors: Bordo, D. / Colnagni, R. / Deriu, D. / Carpen, A. / Pagani, S. / Bolognesi, M.
History
DepositionMar 23, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SULFURTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0868
Polymers29,6961
Non-polymers3897
Water6,143341
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)40.310, 150.310, 53.390
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 SULFURTRANSFERASE / RHODANESE


Mass: 29696.475 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AZOTOBACTER VINELANDII (bacteria) / Description: SYNTHETIC GENE / Cellular location: CYTOPLASM / Gene: RHDA / Plasmid: PQE32 / Cellular location (production host): CYTOPLASM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15 / Variant (production host): PRE4 / References: UniProt: P52197, thiosulfate sulfurtransferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / 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: 3 Å3/Da / Density % sol: 50 %
Crystal growpH: 7.5 / Details: 1.8 M MGSO4 50 MM MES PH 6.0, 5% (V/V)ETHANEDIOL
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
230 mMammonium sulfate1reservoir
33 mM1reservoirNaN3
45 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 1
DetectorType: MARRESEARCH / Date: Jul 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 30532 / % possible obs: 98.5 % / Redundancy: 10.7 % / Rsym value: 0.076 / Net I/σ(I): 8.5
Reflection shellResolution: 1.8→1.85 Å / Rmerge(I) obs: 0.23 / % possible all: 93.6
Reflection
*PLUS
Num. measured all: 328605 / Rmerge(I) obs: 0.076
Reflection shell
*PLUS
% possible obs: 93.6 %

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASESphasing
RefinementMethod to determine structure: MIR / Resolution: 1.8→30 Å / σ(F): 0 / ESU R: 0.12577 / ESU R Free: 0.12558
RfactorNum. reflection% reflectionSelection details
Rfree0.23 3053 10 %RANDOM
Rwork0.18 ---
obs0.18 30532 98.5 %-
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2098 0 21 341 2460
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.007
X-RAY DIFFRACTIONp_angle_d0.006
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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