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- PDB-3olh: Human 3-mercaptopyruvate sulfurtransferase -

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Basic information

Entry
Database: PDB / ID: 3olh
TitleHuman 3-mercaptopyruvate sulfurtransferase
Components3-mercaptopyruvate sulfurtransferase
KeywordsTRANSFERASE / Structural Genomics / Structural Genomics Consortium / SGC / RHODANESE FOLD
Function / homology
Function and homology information


sulfur amino acid catabolic process / 3-mercaptopyruvate sulfurtransferase / 3-mercaptopyruvate sulfurtransferase activity / cyanate catabolic process / Degradation of cysteine and homocysteine / thiosulfate sulfurtransferase activity / hydrogen sulfide biosynthetic process / transsulfuration / spinal cord development / liver development ...sulfur amino acid catabolic process / 3-mercaptopyruvate sulfurtransferase / 3-mercaptopyruvate sulfurtransferase activity / cyanate catabolic process / Degradation of cysteine and homocysteine / thiosulfate sulfurtransferase activity / hydrogen sulfide biosynthetic process / transsulfuration / spinal cord development / liver development / kidney development / response to toxic substance / mitochondrial matrix / neuron projection / synapse / mitochondrion / extracellular exosome / identical protein binding
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
3-mercaptopyruvate sulfurtransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKarlberg, T. / Collins, R. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. ...Karlberg, T. / Collins, R. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Kotenyova, T. / Kouznetsova, E. / Moche, M. / Nordlund, P. / Nyman, T. / Persson, C. / Schutz, P. / Sehic, A. / Siponen, M.I. / Thorsell, A.G. / Tresaugues, L. / Van Den Berg, S. / Wahlberg, E. / Weigelt, J. / Welin, M. / Schuler, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Human 3-Mercaptopyruvate Sulfurtransferase
Authors: Karlberg, T. / Collins, R. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Kotenyova, T. / ...Authors: Karlberg, T. / Collins, R. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Kotenyova, T. / Kouznetsova, E. / Moche, M. / Nordlund, P. / Nyman, T. / Persson, C. / Sehic, A. / Schutz, P. / Siponen, M.I. / Thorsell, A.G. / Tresaugues, L. / Van Den Berg, S. / Wahlberg, E. / Weigelt, J. / Welin, M. / Schuler, H.
History
DepositionAug 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: 3-mercaptopyruvate sulfurtransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2004
Polymers33,9851
Non-polymers2153
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)171.314, 171.314, 75.764
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein 3-mercaptopyruvate sulfurtransferase / MST


Mass: 33985.125 Da / Num. of mol.: 1 / Fragment: UNP residuse 11-289
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MPST, TST2 / Plasmid: PNIC-BSA4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) R3 pRARE
References: UniProt: P25325, 3-mercaptopyruvate sulfurtransferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.15 Å3/Da / Density % sol: 60.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 3.9
Details: 1.5M Ammonium sulfate, 0.1M Sodium acetate , pH 3.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Feb 18, 2010 / Details: Mirrors and double crystal monochromator
RadiationMonochromator: Double crystal (Si-111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.5→35 Å / Num. all: 14710 / Num. obs: 14710 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.1 % / Biso Wilson estimate: 47.07 Å2 / Rmerge(I) obs: 0.115 / Rsym value: 0.093 / Net I/σ(I): 22.2
Reflection shellResolution: 2.5→2.57 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.697 / Mean I/σ(I) obs: 3.7 / Rsym value: 0.508 / % possible all: 97.2

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Processing

Software
NameVersionClassification
MAR345data collection
BALBESphasing
BUSTER2.9.2refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BOI

1boi


Resolution: 2.5→33.74 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.8639 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2701 1471 10 %RANDOM
Rwork0.2212 ---
obs0.2261 14710 100 %-
all-14710 --
Displacement parametersBiso mean: 57.88 Å2
Baniso -1Baniso -2Baniso -3
1--0.5885 Å20 Å20 Å2
2---0.5885 Å20 Å2
3---1.1769 Å2
Refine analyzeLuzzati coordinate error obs: 0.522 Å
Refinement stepCycle: LAST / Resolution: 2.5→33.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2139 0 11 75 2225
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0092210HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.993008HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d966SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes44HARMONIC2
X-RAY DIFFRACTIONt_gen_planes333HARMONIC5
X-RAY DIFFRACTIONt_it2210HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.31
X-RAY DIFFRACTIONt_other_torsion2.82
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2745
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact25284
LS refinement shellResolution: 2.5→2.7 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.3239 293 10 %
Rwork0.2534 2636 -
all0.2601 2929 -
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.40690.4162-0.19878.5961.12121.71090.35-0.3282-0.49431.82660.1449-1.01830.8392-0.057-0.49490.3145-0.0701-0.4218-0.4664-0.0133-0.315-40.5851-34.9069-32.0721
24.39243.0043-2.32867.0034-0.06040.71920.1428-0.4793-0.59542.1145-0.0256-1.43330.93950.2056-0.11720.70970.0223-0.558-0.3690.0545-0.1453-39.0437-32.7595-27.7639
31.22181.48210.91176.83872.23392.54680.41310.0176-0.21731.22970.0207-1.01240.51170.1839-0.43380.07940.0226-0.1989-0.2578-0.0519-0.1028-36.7692-12.7511-33.8311
4-1.55330.9053-1.60251.56312.63621.10990.0504-0.0199-0.077-0.1367-0.06390.13620.09750.02150.01350.24970.1814-0.05-0.27360.022-0.2667-45.5209-4.5824-49.1682
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|7 - 87}A7 - 87
2X-RAY DIFFRACTION2{A|88 - 162}A88 - 162
3X-RAY DIFFRACTION3{A|163 - 282}A163 - 282
4X-RAY DIFFRACTION4{A|283 - 287}A283 - 287

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