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- PDB-4jgt: Structure and kinetic analysis of H2S production by human Mercapt... -

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Basic information

Entry
Database: PDB / ID: 4jgt
TitleStructure and kinetic analysis of H2S production by human Mercaptopyruvate Sulfurtransferase
Components3-mercaptopyruvate sulfurtransferase
KeywordsTRANSFERASE / Rhodanese / 3-mercaptopyruvate sulfurtransferase
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
PYRUVIC ACID / 3-mercaptopyruvate sulfurtransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.161 Å
AuthorsKoutmos, M. / Yamada, K. / Yadav, P.K. / Chiku, T. / Banerjee, R.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structure and Kinetic Analysis of H2S Production by Human Mercaptopyruvate Sulfurtransferase.
Authors: Yadav, P.K. / Yamada, K. / Chiku, T. / Koutmos, M. / Banerjee, R.
History
DepositionMar 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2013Group: Database references
Revision 1.2Jun 19, 2013Group: Derived calculations
Revision 1.3Jul 24, 2013Group: Database references
Revision 1.4Sep 20, 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_conn / 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_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-mercaptopyruvate sulfurtransferase
B: 3-mercaptopyruvate sulfurtransferase
C: 3-mercaptopyruvate sulfurtransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,62115
Polymers100,4963
Non-polymers1,12512
Water6,341352
1
A: 3-mercaptopyruvate sulfurtransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8755
Polymers33,4991
Non-polymers3764
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 3-mercaptopyruvate sulfurtransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6833
Polymers33,4991
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 3-mercaptopyruvate sulfurtransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0637
Polymers33,4991
Non-polymers5646
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)110.737, 171.859, 72.984
Angle α, β, γ (deg.)90.00, 117.18, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 3-mercaptopyruvate sulfurtransferase / MST


Mass: 33498.621 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MPST, TST2 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P25325, 3-mercaptopyruvate sulfurtransferase
#2: Chemical ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H4O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / 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: 3.07 Å3/Da / Density % sol: 59.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 2 M ammonium sulfate, 0.1 M sodium acetate pH 4.5 and 0.02 M betaine hydrochloride, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 8, 2012
Details: K-B pair of biomorph mirrors for vertical and horizontal focusing
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.15→85.93 Å / Num. all: 61916 / Num. obs: 59501 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Biso Wilson estimate: 40.3 Å2 / Rsym value: 0.074 / Net I/σ(I): 6.8
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 4918 / Rsym value: 0.036 / % possible all: 96.1

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3OLH

3olh


Resolution: 2.161→85.93 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.737 / SU ML: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.198 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21997 3121 5 %RANDOM
Rwork0.1855 ---
obs0.18727 58794 95.63 %-
all-61590 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.737 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å2-0.16 Å2
2--1.17 Å20 Å2
3----1.13 Å2
Refinement stepCycle: LAST / Resolution: 2.161→85.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6620 0 64 352 7036
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0196871
X-RAY DIFFRACTIONr_bond_other_d0.0010.026356
X-RAY DIFFRACTIONr_angle_refined_deg1.3841.9549338
X-RAY DIFFRACTIONr_angle_other_deg0.783.00114476
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1335830
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.68322.669341
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.013151038
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7441565
X-RAY DIFFRACTIONr_chiral_restr0.0790.2955
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217818
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021641
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.161→2.217 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 169 -
Rwork0.27 3066 -
obs--67.92 %

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