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- PDB-2wlr: Putative thiosulfate sulfurtransferase YnjE -

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Basic information

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


thiosulfate sulfurtransferase / sulfurtransferase activity / thiosulfate 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 / MAD / Resolution: 1.45 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 25, 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 1.2Mar 13, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other / Refinement description
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / refine / struct_biol / struct_conn
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _refine.pdbx_starting_model / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

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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)48,2883
Polymers47,8121
Non-polymers4772
Water9,908550
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)37.330, 84.010, 132.410
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


Mass: 47811.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SE-MET DERIVATIVE / 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 / HEPES


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


Mass: 18.015 Da / Num. of mol.: 550 / Source method: isolated from a natural source / Formula: H2O
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: 278 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: HANGING DROP, TEMPERATURE 5 C, PEG10000 20%(W/V), HEPES 0.1M PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1.03317
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 8, 2009 / Details: MIRROR 2 VERTICALLY FOCUSSING
RadiationMonochromator: DOUBLE CRYSTAL SI(111), HORIZONTALLY FOCUSSING
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 1.45→24.7 Å / Num. obs: 74519 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 11.7 % / Biso Wilson estimate: 20.4 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 19.6
Reflection shellResolution: 1.45→1.6 Å / Redundancy: 6 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.9 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0070refinement
XDSdata reduction
XSCALEdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: MAD / Resolution: 1.45→23.76 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.121 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.19599 2550 3.4 %RANDOM
Rwork0.17485 ---
obs0.1756 71962 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.789 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2---0.58 Å20 Å2
3---0.66 Å2
Refinement stepCycle: LAST / Resolution: 1.45→23.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3210 0 30 550 3790
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223331
X-RAY DIFFRACTIONr_bond_other_d0.0010.022260
X-RAY DIFFRACTIONr_angle_refined_deg1.4611.9484534
X-RAY DIFFRACTIONr_angle_other_deg0.93735515
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7675407
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.6224.533150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.54815536
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7971516
X-RAY DIFFRACTIONr_chiral_restr0.0860.2471
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213693
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02646
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_it0.8261.52031
X-RAY DIFFRACTIONr_mcbond_other0.2321.5823
X-RAY DIFFRACTIONr_mcangle_it1.48523257
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.31731300
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5564.51277
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: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 177 -
Rwork0.24 5169 -
obs--98.07 %

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