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- PDB-1h4k: Sulfurtransferase from Azotobacter vinelandii in complex with hyp... -

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Basic information

Entry
Database: PDB / ID: 1h4k
TitleSulfurtransferase from Azotobacter vinelandii in complex with hypophosphite
ComponentsSULFURTRANSFERASE
KeywordsTRANSFERASE / SULFUR METABOLISM / THIOSULFATE:CYANIDE
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-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
HYPOPHOSPHITE / Thiosulfate sulfurtransferase
Similarity search - Component
Biological speciesAZOTOBACTER VINELANDII (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 / Refinement description / 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: SULFURTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0446
Polymers29,6641
Non-polymers3795
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.295, 151.465, 53.638
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-LIKE PROTEIN


Mass: 29664.412 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 M15 (bacteria) / Variant (production host): PRE4 / References: UniProt: P52197, thiosulfate sulfurtransferase
#2: Chemical ChemComp-PO2 / HYPOPHOSPHITE / Phosphinate


Mass: 62.973 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2P
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


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


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O
Compound detailsOTHER_DETAILS: HYPOPHOSPHYTE BOUND IN FRONT OF THE ACTIVE SITE. SIMILARITY: RHODANESE FAMILY MEMBER.

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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

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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→30 Å / Num. obs: 18208 / % possible obs: 92.4 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 10.5
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 2 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3.8 / Rsym value: 0.3 / % possible all: 90.2

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Processing

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

1e0c


Resolution: 2.05→30 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.24 --RANDOM
Rwork0.21 ---
obs0.21 19795 92.5 %-
Refinement stepCycle: LAST / Resolution: 2.05→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2098 0 21 196 2315
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_deg3.5
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
Xplor fileSerial no: 1 / Param file: PARAM19X.PRO

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