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- PDB-4chl: Human Ethylmalonic Encephalopathy Protein 1 (hETHE1) -

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Basic information

Entry
Database: PDB / ID: 4chl
TitleHuman Ethylmalonic Encephalopathy Protein 1 (hETHE1)
ComponentsPERSULFIDE DIOXYGENASE ETHE1, MITOCHONDRIAL
KeywordsOXIDOREDUCTASE / SULFIDE DETOXIFICATION / GLYOXALASE II FAMILY
Function / homology
Function and homology information


persulfide dioxygenase / hydrogen sulfide metabolic process / sulfur dioxygenase activity / Sulfide oxidation to sulfate / glutathione metabolic process / mitochondrial matrix / iron ion binding / mitochondrion / nucleoplasm / identical protein binding / cytoplasm
Similarity search - Function
Persulfide dioxygenase-like, MBL-fold metallo-hydrolase domain / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Persulfide dioxygenase ETHE1, mitochondrial
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsPettinati, I. / Brem, J. / McDonough, M.A. / Schofield, C.J.
CitationJournal: Hum. Mol. Genet. / Year: 2015
Title: Crystal structure of human persulfide dioxygenase: structural basis of ethylmalonic encephalopathy.
Authors: Pettinati, I. / Brem, J. / McDonough, M.A. / Schofield, C.J.
History
DepositionDec 3, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 28, 2015Group: Database references
Revision 1.2Apr 15, 2015Group: Database references
Revision 1.3Mar 14, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _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_atom_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: PERSULFIDE DIOXYGENASE ETHE1, MITOCHONDRIAL
B: PERSULFIDE DIOXYGENASE ETHE1, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4694
Polymers52,3582
Non-polymers1122
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-37.5 kcal/mol
Surface area19310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.940, 124.930, 63.090
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 PERSULFIDE DIOXYGENASE ETHE1, MITOCHONDRIAL / ETHYLMALONIC ENCEPHALOPATHY PROTEIN 1 / SULFUR DIOXYGENASE ETHE1 / PERSULFIDE DIOXYGENASE


Mass: 26178.863 Da / Num. of mol.: 2 / Fragment: METALLO BETA-LACTAMASE, RESIDUES 21-254
Source method: isolated from a genetically manipulated source
Details: RESIDUE CYS247 MODELLED AS SULFINIC ACID / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PCOLD / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O95571, persulfide dioxygenase
#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.85 Å3/Da / Density % sol: 56.87 % / Description: NONE
Crystal growpH: 8.5
Details: 10 MG/ML PROTEIN IN 50MM HEPES PH7.5, 100 MM NACL ADDED TO 0.1M TRIS-HCL PH8.5, 0.5M POTASSIUM THIOCYANATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.07188
DetectorType: DECTRIS HYBRID / Detector: PIXEL / Date: Oct 17, 2013 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07188 Å / Relative weight: 1
ReflectionResolution: 2.61→73.94 Å / Num. obs: 18351 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 41.77 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 13.7
Reflection shellResolution: 2.61→2.68 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 1.9 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GCU

2gcu


Resolution: 2.61→63.631 Å / SU ML: 0.26 / σ(F): 1.34 / Phase error: 23.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2232 936 5.1 %
Rwork0.1785 --
obs0.1808 18307 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.61→63.631 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3598 0 2 132 3732
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053688
X-RAY DIFFRACTIONf_angle_d0.7425027
X-RAY DIFFRACTIONf_dihedral_angle_d13.9661342
X-RAY DIFFRACTIONf_chiral_restr0.041579
X-RAY DIFFRACTIONf_plane_restr0.003654
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.61-2.74760.32341390.24982415X-RAY DIFFRACTION99
2.7476-2.91980.29751260.2362437X-RAY DIFFRACTION100
2.9198-3.14520.26041350.20792450X-RAY DIFFRACTION100
3.1452-3.46170.23211350.19562454X-RAY DIFFRACTION100
3.4617-3.96250.20521310.16722478X-RAY DIFFRACTION100
3.9625-4.99210.21420.1382505X-RAY DIFFRACTION100
4.9921-63.64950.18951280.16872632X-RAY DIFFRACTION99
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)
10.02170.1237-0.0370.2875-0.22240.0930.32810.05840.1092-0.3712-0.1151-0.15510.36830.40870.00610.3511-0.002-0.02730.477-0.01920.484414.4397-47.7197-10.236
20.0843-0.11350.13720.2605-0.0395-0.01490.2667-0.31670.1607-0.0141-0.179-0.04710.0082-0.1192-0.00010.39710.02460.00290.369-0.03380.345413.3208-52.537-15.8852
30.0733-0.04410.00530.05850.02990.0143-0.26750.2851-0.1004-0.54750.4516-0.3160.12960.0194-0.00020.60510.0079-0.00050.4276-0.04010.321314.1637-47.7607-24.744
4-0.0033-0.06230.00690.1889-0.24470.2669-0.09920.2676-0.0528-0.45930.1131-0.09070.27130.1428-00.4292-0.0201-0.00320.4-0.04530.36312.697-58.4877-20.3948
50.40610.0652-0.11160.2910.10930.0897-0.06180.0779-0.27090.01710.0308-0.50670.22150.15620.00010.43050.0220.06760.3875-0.01540.45617.7236-63.9839-17.1041
60.372-0.1327-0.36090.2606-0.17420.6175-0.06680.29120.0940.0917-0.01670.29450.15480.05590.00010.3914-0.02140.00320.3782-0.0090.37363.8412-64.0775-9.9674
70.4315-0.1425-0.11670.34720.48450.4050.0039-0.0010.20310.3144-0.10570.23140.0773-0.1472-00.475-0.01210.0410.386-0.01520.35280.356-60.8145-2.754
80.3291-0.1017-0.49680.33150.00260.47850.16010.27190.0940.053-0.00470.2195-0.1054-0.2360.02790.4693-0.0570.01930.5254-0.02630.435-3.6568-67.2411-20.2102
9-0.00150.1830.11350.3135-0.08560.0515-0.2134-0.1274-0.53390.12410.0518-0.17750.3105-0.2434-0.01260.40380.03260.02580.3343-0.02590.52326.0142-44.4444-1.1042
100.46480.2338-0.26460.2021-0.06690.1529-0.1724-0.1364-0.0697-0.0639-0.1579-0.07430.3203-0.04630.00010.35180.0226-0.01520.33310.01240.338-0.5411-39.3918-2.8728
110.7168-0.1786-0.20670.37640.05840.28080.059-0.06090.08450.31770.1820.5697-0.1042-0.23400.35630.00820.01220.44350.00250.4607-7.6944-35.0259-2.1316
120.94390.1962-0.58532.1576-0.51411.43160.05420.00510.0742-0.0613-0.0308-0.1317-0.030.100100.2447-0.0037-0.0010.29380.0070.34137.8307-28.9764-10.9359
130.8441-0.2570.31210.55880.07660.12480.14080.32280.2093-0.09490.00510.2658-0.1273-0.337500.39720.02580.00930.53790.0550.4883-5.8967-26.0412-20.0904
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 18 THROUGH 30 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 31 THROUGH 54 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 55 THROUGH 67 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 68 THROUGH 87 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 88 THROUGH 131 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 132 THROUGH 170 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 171 THROUGH 218 )
8X-RAY DIFFRACTION8CHAIN A AND (RESID 219 THROUGH 252 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 17 THROUGH 30 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 31 THROUGH 54 )
11X-RAY DIFFRACTION11CHAIN B AND (RESID 55 THROUGH 106 )
12X-RAY DIFFRACTION12CHAIN B AND (RESID 107 THROUGH 218 )
13X-RAY DIFFRACTION13CHAIN B AND (RESID 219 THROUGH 254 )

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