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- PDB-1h4m: Sulfurtransferase from Azotobacter vinelandii in complex with pho... -

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Basic information

Entry
Database: PDB / ID: 1h4m
TitleSulfurtransferase from Azotobacter vinelandii in complex with phosphate
ComponentsPUTATIVE THIOSULFATE SULFURTRANSFERASE
KeywordsTRANSFERASE / SULFUR METABOLISM / THIOSULFATE:CYANIDE
Function / homology
Function and homology information


thiosulfate sulfurtransferase / thiosulfate-cyanide 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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBordo, D. / Forlani, F. / Spallarossa, A. / Colnaghi, R. / Carpen, A. / Pagani, S. / Bolognesi, M.
Citation
Journal: Biol.Chem. / Year: 2001
Title: A Persulfurated Cysteine Promotes Active Site Reactivity in Azotobacter Vinelandii Rhodanse
Authors: Bordo, D. / Forlani, F. / Spallarossa, A. / Colnaghi, R. / Carpen, A. / Bolognesi, M. / Pagani, S.
#1: Journal: J.Mol.Biol. / Year: 2000
Title: The Crystal Structure of a Sulfurtransferase from Azotobacter Vinelandii Highliths the Evolutionary Relationship between the Rhodanese and Phosphatase Enzyme Families
Authors: Bordo, D. / Deriu, D. / Colnaghi, R. / Carpen, A. / Pagani, S. / Bolognesi, M.
History
DepositionMay 11, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2002Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
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_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 / _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

Downloads & links

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Assembly

Deposited unit
X: PUTATIVE THIOSULFATE SULFURTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7893
Polymers29,6641
Non-polymers1242
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.410, 151.469, 53.609
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 PUTATIVE THIOSULFATE SULFURTRANSFERASE / RHODANESE-LIKE PROTEIN


Mass: 29664.412 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AZOTOBACTER VINELANDII (bacteria) / Cellular location: CYTOPLASM / Gene: RHDA / Plasmid: PQE32 / Cellular location (production host): CYTOPLASM / Production host: ESCHERICHIA COLI M15 (bacteria) / Variant (production host): PRE4 / References: UniProt: P52197, thiosulfate sulfurtransferase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 6.5
Details: 1.7 M MGSO4, 50 MM MES PH 6.0, 5% (V/V)ETHANEDIOL. NATIVE RHDA CRYSTALS SOAKED IN 5 MM AMMONIUM HYDROGEN PHOSPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8349
DetectorType: MARRESEARCH
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8349 Å / Relative weight: 1
ReflectionResolution: 2.05→19.2 Å / Num. obs: 15806 / % possible obs: 73.7 % / Redundancy: 18.2 % / Rmerge(I) obs: 0.032 / Net I/σ(I): 26.9
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 2 % / Rmerge(I) obs: 0.046 / Mean I/σ(I) obs: 24 / % possible all: 68.6

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E0C

1e0c


Resolution: 2.1→20 Å / SU B: 4.77755 / SU ML: 0.13366 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.22665 / Details: NONE
RfactorNum. reflection% reflectionSelection details
Rfree0.25023 799 5.1 %RANDOM
Rwork0.17403 ---
obs0.17793 15007 73.8 %-
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2097 0 8 201 2306

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