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- PDB-1boh: SULFUR-SUBSTITUTED RHODANESE (ORTHORHOMBIC FORM) -

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Basic information

Entry
Database: PDB / ID: 1boh
TitleSULFUR-SUBSTITUTED RHODANESE (ORTHORHOMBIC FORM)
ComponentsRHODANESE
KeywordsTRANSFERASE / RHODANESE / SULFURTRANSFERASE
Function / homology
Function and homology information


rRNA transport / 3-mercaptopyruvate sulfurtransferase activity / thiosulfate sulfurtransferase / thiosulfate-cyanide sulfurtransferase activity / rRNA import into mitochondrion / 5S rRNA binding / mitochondrial matrix / mitochondrion
Similarity search - Function
Sulfurtransferase TST/MPST-like / 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 ...Sulfurtransferase TST/MPST-like / 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 speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGliubich, F. / Berni, R. / Cianci, M. / Trevino, R.J. / Horowitz, P.M. / Zanotti, G.
Citation
Journal: J.Biol.Chem. / Year: 1999
Title: NH2-terminal sequence truncation decreases the stability of bovine rhodanese, minimally perturbs its crystal structure, and enhances interaction with GroEL under native conditions.
Authors: Trevino, R.J. / Gliubich, F. / Berni, R. / Cianci, M. / Chirgwin, J.M. / Zanotti, G. / Horowitz, P.M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Structure of Sulfur-Substituted Rhodanese at 1.36 A Resolution
Authors: Gliubich, F. / Berni, R. / Colapietro, M. / Barba, L. / Zanotti, G.
#2: Journal: J.Biol.Chem. / Year: 1996
Title: Active Site Structural Features for Chemically Modified Forms of Rhodanese
Authors: Gliubich, F. / Gazerro, M. / Zanotti, G. / Delbono, S. / Bombieri, G. / Berni, R.
#3: Journal: J.Mol.Biol. / Year: 1979
Title: The Structure of Bovine Liver Rhodanese. II. The Active Site in the Sulfur-Substituted and the Sulfur-Free Enzyme
Authors: Ploegman, J.H. / Drent, G. / Kalk, K.H. / Hol, W.G.
History
DepositionAug 4, 1998Processing site: BNL
Revision 1.0Apr 27, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Revision 1.4Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RHODANESE


Theoretical massNumber of molelcules
Total (without water)33,2411
Polymers33,2411
Non-polymers00
Water1,13563
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.740, 72.350, 39.070
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 RHODANESE


Mass: 33240.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SULFUR SUBSTITUTED AT RESIDUE CYS 247 / Source: (gene. exp.) Bos taurus (domestic cattle) / Cellular location: CYTOPLASM / Organ: LIVER / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P00586, thiosulfate sulfurtransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 37 %
Crystal growpH: 7.3 / Details: pH 7.3
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14 mg/mlprotein1drop
210 %(w/v)PEG60001drop
350 mMTris-HCl1drop
450 mMsodium acetate1drop
51 mMsodium thiosulfate1drop
616 %(w/v)PEG60001reservoir
750 mMTris-HCl1reservoir
850 mMsodium acetate1reservoir
91 mMsodium thiosulfate1reservoir

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Data collection

DiffractionMean temperature: 297 K
Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Oct 1, 1997
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→55 Å / Num. obs: 10362 / % possible obs: 78.8 % / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Rmerge(I) obs: 0.11 / Rsym value: 0.11
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.34 / Rsym value: 0.24 / % possible all: 13.4
Reflection
*PLUS
Num. measured all: 60362

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.83refinement
XENGENdata reduction
SAINTdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RHS

1rhs


Resolution: 2.3→55 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.0001 / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.215 548 5 %EVERY 5TH REFLECTION
Rwork0.166 ---
obs0.166 10362 87.3 %-
Refinement stepCycle: LAST / Resolution: 2.3→55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2327 0 0 63 2390
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.02
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.2
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor fileSerial no: 1 / Param file: PARAM19X.PRO / Topol file: TOPH19X.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.83 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.2

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