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- PDB-1rhs: SULFUR-SUBSTITUTED RHODANESE -

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Basic information

Entry
Database: PDB / ID: 1rhs
TitleSULFUR-SUBSTITUTED RHODANESE
ComponentsSULFUR-SUBSTITUTED RHODANESE
KeywordsTRANSFERASE / RHODANESE / SULFURTRANSFERASE
Function / homology
Function and homology information


rRNA transport / 3-mercaptopyruvate sulfurtransferase activity / thiosulfate sulfurtransferase / thiosulfate 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 (cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.36 Å
AuthorsZanotti, G. / Gliubich, F. / Colapietro, M. / Barba, L.
Citation
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.
#1: 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
DepositionJul 16, 1997Processing site: BNL
Revision 1.0Jan 21, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_site / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SULFUR-SUBSTITUTED RHODANESE


Theoretical massNumber of molelcules
Total (without water)33,2411
Polymers33,2411
Non-polymers00
Water7,332407
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)154.364, 49.312, 41.676
Angle α, β, γ (deg.)90.00, 99.81, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein SULFUR-SUBSTITUTED RHODANESE


Mass: 33240.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Cellular location: CYTOPLASM / Organ: LIVER / References: UniProt: P00586, thiosulfate sulfurtransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 407 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49 %
Crystal growpH: 7.6 / Details: pH 7.6
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.4 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.9 Mammonium sulfate1reservoir
230 mMsodium phosphate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceWavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE AREA DETECTOR / Date: Jul 1, 1996 / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.36→25 Å / Num. obs: 56060 / % possible obs: 74 % / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 22.6
Reflection shellResolution: 1.3→1.4 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.7 / Rsym value: 0.33 / % possible all: 45
Reflection
*PLUS
Num. measured all: 131477
Reflection shell
*PLUS
Highest resolution: 1.36 Å / Lowest resolution: 1.43 Å / % possible obs: 45 % / Num. unique obs: 10176

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Processing

Software
NameClassification
SHELXL-93model building
SHELXL-93refinement
XDSdata reduction
MARSCALEdata scaling
SHELXL-93phasing
RefinementResolution: 1.36→25 Å / Num. parameters: 24750 / Num. restraintsaints: 29262 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: SHELXL
RfactorNum. reflection% reflectionSelection details
Rfree0.2289 2792 5 %EVERY 5TH REFLECTION
all0.1694 5582 --
obs0.159 -74 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 8872 / Occupancy sum non hydrogen: 11056
Refinement stepCycle: LAST / Resolution: 1.36→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2327 0 0 407 2734
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.03
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.2
X-RAY DIFFRACTIONs_zero_chiral_vol0.2
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.2
X-RAY DIFFRACTIONs_anti_bump_dis_restr0
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-93 / Classification: refinement
Refinement
*PLUS
Num. reflection all: 53034
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.2
X-RAY DIFFRACTIONs_chiral_restr0.2

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