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- PDB-1okg: 3-mercaptopyruvate sulfurtransferase from Leishmania major -

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Basic information

Entry
Database: PDB / ID: 1okg
Title3-mercaptopyruvate sulfurtransferase from Leishmania major
ComponentsPOSSIBLE 3-MERCAPTOPYRUVATE SULFURTRANSFERASE
KeywordsTRANSFERASE / MERCAPTOPYRUVATE / SULFURTRANSFERASE / RHODANESE / PROLYL ISOMERASE / CATALYTIC TRIAD / SERINE PROTEASE / LEISHMANIA PYRUVATE
Function / homology
Function and homology information


3-mercaptopyruvate sulfurtransferase / 3-mercaptopyruvate sulfurtransferase activity / cyanide metabolic process / cysteine biosynthetic process via cystathionine / thiosulfate sulfurtransferase activity / transsulfuration / cytosol
Similarity search - Function
3-mercaptopyruvate sulfurtransferase, domain 3 / 3-mercaptopyruvate sulfurtransferase, domain 3 / 3-mercaptopyruvate sulfurtransferase, C-terminal domain / 3-mercaptopyruvate sulfurtransferase, C-terminal domain superfamily / Domain of unknown function (DUF1930) / Rhodanese-like domain / Oxidized Rhodanese; domain 1 / Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. ...3-mercaptopyruvate sulfurtransferase, domain 3 / 3-mercaptopyruvate sulfurtransferase, domain 3 / 3-mercaptopyruvate sulfurtransferase, C-terminal domain / 3-mercaptopyruvate sulfurtransferase, C-terminal domain superfamily / Domain of unknown function (DUF1930) / Rhodanese-like domain / Oxidized Rhodanese; domain 1 / Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
SULFITE ION / 3-mercaptopyruvate sulfurtransferase / :
Similarity search - Component
Biological speciesLEISHMANIA MAJOR (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.1 Å
AuthorsAlphey, M.S. / Hunter, W.N.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: The Crystal Structure of Leishmania Major 3-Mercaptopyruvate Sulfurtransferase: A Three-Domain Architecture with a Serine Protease-Like Triad at the Active Site
Authors: Alphey, M.S. / Williams, R.A.M. / Mottram, J.C. / Coombs, G.H. / Hunter, W.N.
History
DepositionJul 24, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: POSSIBLE 3-MERCAPTOPYRUVATE SULFURTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4183
Polymers41,2981
Non-polymers1202
Water7,278404
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)109.574, 109.574, 67.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein POSSIBLE 3-MERCAPTOPYRUVATE SULFURTRANSFERASE / MERCAPTOPYRUVATE SULFURTRANSFERASE


Mass: 41297.684 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LEISHMANIA MAJOR (eukaryote) / Plasmid: PET22A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834
References: UniProt: Q9NE49, UniProt: Q7K9G0*PLUS, 3-mercaptopyruvate sulfurtransferase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SO3 / SULFITE ION / Sulfite


Mass: 80.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 404 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUES ALA 367 VAL
Sequence detailsRESIDUES 371 TO 373 IN THE RECORDS BELOW BELONG TO A SECTION OF THE RECOMBINANT AFFINITY TAG, AND ...RESIDUES 371 TO 373 IN THE RECORDS BELOW BELONG TO A SECTION OF THE RECOMBINANT AFFINITY TAG, AND ARE THEREFORE MAPPED TO THEMSELVES.

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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: 2.4 Å3/Da / Density % sol: 48 %
Crystal growpH: 8 / Details: pH 8.00
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
13.5 mg/mlprotein1drop
214 %(w/v)PEG80001reservoir
380 mMsodium cacodylate1reservoirpH6.5
4160 mMcalcium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 21, 2002 / Details: MIRROR
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 23924 / % possible obs: 97.8 % / Redundancy: 5.4 % / Biso Wilson estimate: 36.1 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 23.2
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 4.5 / % possible all: 97.2
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 20 Å / Redundancy: 5.4 % / Num. measured all: 131345 / Rmerge(I) obs: 0.047
Reflection shell
*PLUS
% possible obs: 97.2 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 4.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
MLPHAREphasing
REFMAC5.1.24refinement
RefinementMethod to determine structure: OTHER / Resolution: 2.1→76.7 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.899 / SU B: 5.558 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.254 / ESU R Free: 0.232
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: RESIDUES 1-6 AND IN LOOP 239-243 WERE DISORDERED AND COULD NOT BE MODELED. MOST REFINEMENT CARRIED OUT AGAINST A TRUNCATED DATASET TO AVOID RADIATION DAMAGE EFFECTS.
RfactorNum. reflection% reflectionSelection details
Rfree0.287 1225 5.1 %RANDOM
Rwork0.208 ---
obs0.212 22691 97.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.06 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å20 Å20 Å2
2---0.73 Å20 Å2
3---1.46 Å2
Refinement stepCycle: LAST / Resolution: 2.1→76.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2778 0 5 404 3187
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0212860
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4851.9573893
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3265360
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.10.2424
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022189
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2160.21496
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2316
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2510.261
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3550.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7621.51808
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.40822913
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.10331052
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1174.5980
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: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.305 67
Rwork0.234 1632
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.016
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.7
X-RAY DIFFRACTIONr_plane_restr0.007

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