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- PDB-2wlx: Putative thiosulfate sulfurtransferase YnjE -

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Basic information

Entry
Database: PDB / ID: 2wlx
TitlePutative thiosulfate sulfurtransferase YnjE
ComponentsPUTATIVE THIOSULFATE SULFURTRANSFERASE YNJE
KeywordsTRANSFERASE / RHODANESE DOMAINS
Function / homology
Function and homology information


thiosulfate sulfurtransferase / sulfurtransferase activity / thiosulfate-cyanide sulfurtransferase activity / periplasmic space
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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thiosulfate sulfurtransferase YnjE
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.9 Å
AuthorsDeclercq, J.P. / Smeets, A. / Depuydt, M. / Collet, J.F.
CitationJournal: To be Published
Title: Structural Analysis of Ynje, a Putative Thiosulfate Sulfurtransferase
Authors: Declercq, J.P. / Smeets, A. / Depuydt, M. / Collet, J.F.
History
DepositionJun 26, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2014Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / 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 / _pdbx_entry_details.has_protein_modification / _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

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Assembly

Deposited unit
A: PUTATIVE THIOSULFATE SULFURTRANSFERASE YNJE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7733
Polymers47,2961
Non-polymers4772
Water6,575365
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.400, 83.430, 131.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PUTATIVE THIOSULFATE SULFURTRANSFERASE YNJE / YNJE / A PUTATIVE THIOSULFATE SULFURTRANSFERASE


Mass: 47296.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P78067, thiosulfate sulfurtransferase
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsWITHOUT SIGNAL SEQUENCE

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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: 2.2 Å3/Da / Density % sol: 44 % / Description: NONE
Crystal growTemperature: 291 K / pH: 7.5 / Details: 20% PEG 10000, 0.1M HEPES PH 7.5, TEMP 18 C

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979609
DetectorType: MARRESEARCH SX-165 / Detector: CCD / Date: May 17, 2009 / Details: SECOND CRYSTAL SAGITALLY BENT
RadiationMonochromator: FIRST CRYSTAL FLAT AND N2 COOLED / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979609 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 219109 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 29.4 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.4
Reflection shellResolution: 1.9→2.1 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 4.5 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.5.0070refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.9→39.77 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.917 / SU B: 4.452 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25056 1177 3.5 %RANDOM
Rwork0.19693 ---
obs0.19886 32106 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.27 Å2
Baniso -1Baniso -2Baniso -3
1--1.06 Å20 Å20 Å2
2---2.31 Å20 Å2
3---3.37 Å2
Refinement stepCycle: LAST / Resolution: 1.9→39.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3205 0 30 365 3600
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0213326
X-RAY DIFFRACTIONr_bond_other_d0.0010.022258
X-RAY DIFFRACTIONr_angle_refined_deg1.7421.9484527
X-RAY DIFFRACTIONr_angle_other_deg1.00535510
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4135406
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.01724.533150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.86215536
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3831516
X-RAY DIFFRACTIONr_chiral_restr0.1040.2470
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213686
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02645
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9951.52026
X-RAY DIFFRACTIONr_mcbond_other0.2841.5821
X-RAY DIFFRACTIONr_mcangle_it1.63823249
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.61931300
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.8654.51278
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 79 -
Rwork0.274 2315 -
obs--98.97 %

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