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- PDB-6m35: Crystal structure of sulfur oxygenase reductase from Sulfurisphae... -

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Basic information

Entry
Database: PDB / ID: 6m35
TitleCrystal structure of sulfur oxygenase reductase from Sulfurisphaera tokodaii
ComponentsSulfur oxygenase/reductase
KeywordsOXIDOREDUCTASE / spherical homo 24-mer
Function / homologysulfur oxygenase/reductase / sulfur oxygenase/reductase activity / Sulphur oxygenase reductase / Sulphur oxygenase reductase / Dimeric alpha-beta barrel / metal ion binding / : / Sulfur oxygenase/reductase
Function and homology information
Biological speciesSulfurisphaera tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsSato, Y. / Yabuki, T. / Arakawa, T. / Yamada, C. / Fushinobu, S. / Wakagi, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)24580136 Japan
Japan Agency for Medical Research and Development (AMED)JP20am0101071 Japan
CitationJournal: J Struct Biol X / Year: 2020
Title: Crystallographic and cryogenic electron microscopic structures and enzymatic characterization of sulfur oxygenase reductase from .
Authors: Yuta Sato / Takashi Yabuki / Naruhiko Adachi / Toshio Moriya / Takatoshi Arakawa / Masato Kawasaki / Chihaya Yamada / Toshiya Senda / Shinya Fushinobu / Takayoshi Wakagi /
Abstract: Sulfur oxygenase reductases (SORs) are present in thermophilic and mesophilic archaea and bacteria, and catalyze oxygen-dependent oxygenation and disproportionation of elemental sulfur. SOR has a ...Sulfur oxygenase reductases (SORs) are present in thermophilic and mesophilic archaea and bacteria, and catalyze oxygen-dependent oxygenation and disproportionation of elemental sulfur. SOR has a hollow, spherical homo-24-mer structure and reactions take place at active sites inside the chamber. The crystal structures of SORs from species have been reported. However, the states of the active site components (mononuclear iron and cysteines) and the entry and exit paths of the substrate and products are still in dispute. Here, we report the biochemical and structural characterizations of SORs from the thermoacidophilic archaeon (StSOR) and present high-resolution structures determined by X-ray crystallography and cryogenic electron microscopy (cryo-EM). The crystal structure of StSOR was determined at 1.73 Å resolution. At the catalytic center, iron is ligated to His86, His90, Glu114, and two water molecules. Three conserved cysteines in the cavity are located 9.5-13 Å from the iron and were observed as free thiol forms. A mutational analysis indicated that the iron and one of the cysteines (Cys31) were essential for both activities. The cryo-EM structure was determined at 2.24 Å resolution using an instrument operating at 200 kV. The two structures determined by different methodologies showed similar main chain traces, but the maps exhibited different features at catalytically important components. A possible role of StSOR in the sulfur metabolism of (an obligate aerobe) is discussed based on this study. Given the high resolution achieved in this study, StSOR was shown to be a good benchmark sample for cryo-EM.
History
DepositionMar 2, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2020Group: Database references / Derived calculations / Category: citation / pdbx_struct_conn_angle / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sulfur oxygenase/reductase
B: Sulfur oxygenase/reductase
C: Sulfur oxygenase/reductase
D: Sulfur oxygenase/reductase
E: Sulfur oxygenase/reductase
F: Sulfur oxygenase/reductase
G: Sulfur oxygenase/reductase
H: Sulfur oxygenase/reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)288,14733
Polymers286,1078
Non-polymers2,04025
Water22,6451257
1
A: Sulfur oxygenase/reductase
B: Sulfur oxygenase/reductase
C: Sulfur oxygenase/reductase
D: Sulfur oxygenase/reductase
E: Sulfur oxygenase/reductase
F: Sulfur oxygenase/reductase
G: Sulfur oxygenase/reductase
H: Sulfur oxygenase/reductase
hetero molecules

A: Sulfur oxygenase/reductase
B: Sulfur oxygenase/reductase
C: Sulfur oxygenase/reductase
D: Sulfur oxygenase/reductase
E: Sulfur oxygenase/reductase
F: Sulfur oxygenase/reductase
G: Sulfur oxygenase/reductase
H: Sulfur oxygenase/reductase
hetero molecules

A: Sulfur oxygenase/reductase
B: Sulfur oxygenase/reductase
C: Sulfur oxygenase/reductase
D: Sulfur oxygenase/reductase
E: Sulfur oxygenase/reductase
F: Sulfur oxygenase/reductase
G: Sulfur oxygenase/reductase
H: Sulfur oxygenase/reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)864,44199
Polymers858,32024
Non-polymers6,12075
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area164270 Å2
ΔGint-1243 kcal/mol
Surface area207100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)299.806, 299.806, 299.806
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18B
28C
19B
29D
110B
210E
111B
211F
112B
212G
113B
213H
114C
214D
115C
215E
116C
216F
117C
217G
118C
218H
119D
219E
120D
220F
121D
221G
122D
222H
123E
223F
124E
224G
125E
225H
126F
226G
127F
227H
128G
228H

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 2 - 311 / Label seq-ID: 2 - 311

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14AA
24EE
15AA
25FF
16AA
26GG
17AA
27HH
18BB
28CC
19BB
29DD
110BB
210EE
111BB
211FF
112BB
212GG
113BB
213HH
114CC
214DD
115CC
215EE
116CC
216FF
117CC
217GG
118CC
218HH
119DD
219EE
120DD
220FF
121DD
221GG
122DD
222HH
123EE
223FF
124EE
224GG
125EE
225HH
126FF
226GG
127FF
227HH
128GG
228HH

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28

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Components

#1: Protein
Sulfur oxygenase/reductase


Mass: 35763.344 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7) (archaea)
Strain: DSM 16993 / JCM 10545 / NBRC 100140 / 7 / Gene: sor, ST1127, STK_11270 / Plasmid: pET-17b / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / Variant (production host): AI / References: UniProt: Q972K4, sulfur oxygenase/reductase
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1257 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.92 Å3/Da / Density % sol: 68.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.1
Details: 1.2 M ammonium sulfate, 100 mM MES-NaOH (pH 6.1), 4% dioxane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 27, 2019
RadiationMonochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.73→48.7 Å / Num. obs: 460150 / % possible obs: 100 % / Redundancy: 20.7 % / Biso Wilson estimate: 21.484 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.028 / Net I/σ(I): 17.4
Reflection shellResolution: 1.73→1.76 Å / Redundancy: 19.5 % / Rmerge(I) obs: 2.112 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 22755 / CC1/2: 0.626 / Rpim(I) all: 0.491 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CB2

2cb2


Resolution: 1.73→48.68 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.964 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.07
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1792 23051 5 %RANDOM
Rwork0.162 ---
obs0.1629 437088 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 101.29 Å2 / Biso mean: 27.21 Å2 / Biso min: 17.28 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.73→48.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20040 0 103 1257 21400
Biso mean--45.73 35.06 -
Num. residues----2480
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01320702
X-RAY DIFFRACTIONr_bond_other_d0.0350.01718988
X-RAY DIFFRACTIONr_angle_refined_deg1.6881.64628076
X-RAY DIFFRACTIONr_angle_other_deg2.2881.56544116
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.12252472
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.49422.6871072
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.993153488
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.86315104
X-RAY DIFFRACTIONr_chiral_restr0.0980.22520
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0222920
X-RAY DIFFRACTIONr_gen_planes_other0.0170.024368
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A106430.02
12B106430.02
21A106650.02
22C106650.02
31A106460.02
32D106460.02
41A106410.02
42E106410.02
51A106670.02
52F106670.02
61A106540.02
62G106540.02
71A106560.02
72H106560.02
81B106710.02
82C106710.02
91B106240.02
92D106240.02
101B106670.02
102E106670.02
111B106420.02
112F106420.02
121B106700.02
122G106700.02
131B106740.02
132H106740.02
141C106440.02
142D106440.02
151C106870.02
152E106870.02
161C106660.02
162F106660.02
171C106920.02
172G106920.02
181C106930.01
182H106930.01
191D106380.02
192E106380.02
201D106550.02
202F106550.02
211D106410.03
212G106410.03
221D106470.02
222H106470.02
231E106550.02
232F106550.02
241E106800.02
242G106800.02
251E106830.02
252H106830.02
261F106610.02
262G106610.02
271F106580.02
272H106580.02
281G106870.02
282H106870.02
LS refinement shellResolution: 1.73→1.775 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 1668 -
Rwork0.261 32265 -
all-33933 -
obs--100 %

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