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- PDB-6qkm: Diallyl trisulfide inhibited sulfur oxygenase reductase -

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Basic information

Entry
Database: PDB / ID: 6qkm
TitleDiallyl trisulfide inhibited sulfur oxygenase reductase
Components(Sulfur oxygenase/reductase) x 2
KeywordsOXIDOREDUCTASE / SULFUR OXYGENASE REDUCTASE / 2-HIS-1-CARBOXYLATE FACIAL TRIAD / CYSTEINE PERSULPHURATION / BIOGEOCHEMICAL SULFUR CYCLE
Function / homologysulfur oxygenase/reductase / sulfur oxygenase/reductase activity / Sulphur oxygenase reductase / Sulphur oxygenase reductase / Dimeric alpha-beta barrel / metal ion binding / cytoplasm / : / Sulfur oxygenase/reductase
Function and homology information
Biological speciesAcidianus ambivalens (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.102 Å
AuthorsFrazao, C. / Klezin, A. / Poell, U.
Funding support Portugal, Germany, 2items
OrganizationGrant numberCountry
Foundation for Science and TechnologyLIOA-01-0145-FEDER-007660 Portugal
German Research FoundationKl885-7/1 Germany
Citation
Journal: To Be Published
Title: Multiple sulfane modifications in active-site cysteine thiols of two sulfur oxygenase reductases and analysis of substrate/product channels
Authors: Frazao, C. / Klezin, A.
#1: Journal: Science / Year: 2006
Title: X-ray Structure of a self-compartmentalizing sulfur cycle metalloenzyme.
Authors: Urich, T. / Gomes, C.M. / Kletzin, A. / Frazao, C.
#2: Journal: Front Microbiol / Year: 2011
Title: Substrate pathways and mechanisms of inhibition in the sulfur oxygenase reductase of acidianus ambivalens.
Authors: Veith, A. / Urich, T. / Seyfarth, K. / Protze, J. / Frazao, C. / Kletzin, A.
History
DepositionJan 29, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,51013
Polymers219,1196
Non-polymers3917
Water14,610811
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
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
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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)878,04152
Polymers876,47724
Non-polymers1,56428
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area137700 Å2
ΔGint-1146 kcal/mol
Surface area206880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.012, 162.012, 153.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Sulfur oxygenase/reductase / Sulfur oxygenase reductase / SOR


Mass: 36541.262 Da / Num. of mol.: 2 / Mutation: TSY, CSS
Source method: isolated from a genetically manipulated source
Details: In chains A and D residues CYS_31 appear derivatized into TSY_31, residues CYS_101 appear derivatized into TSY_101 and residues CYS_104 appear derivatized into CSS_104, by chemical modification.
Source: (gene. exp.) Acidianus ambivalens (archaea) / Gene: sor / Production host: Escherichia coli (E. coli) / References: UniProt: P29082, sulfur oxygenase/reductase
#2: Protein
Sulfur oxygenase/reductase / Sulfur oxygenase reductase / SOR


Mass: 36509.195 Da / Num. of mol.: 4 / Mutation: CSS
Source method: isolated from a genetically manipulated source
Details: In chains B, C, E and F residues CYS_31 appear derivatized into TSY_31, residues CYS_101 appear derivatized into CSS_101 and residues CYS_104 appear derivatized into CSS_104, by chemical modification.
Source: (gene. exp.) Acidianus ambivalens (archaea) / Gene: sor / Production host: Escherichia coli (E. coli) / References: UniProt: P29082, sulfur oxygenase/reductase
#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 811 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.3 Å3/Da / Density % sol: 46.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0.1 M sodium acetate pH 4.6, 2 M sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→76.9 Å / Num. obs: 226318 / % possible obs: 99.3 % / Redundancy: 3.4 % / Biso Wilson estimate: 35 Å2 / CC1/2: 0.995 / Rpim(I) all: 0.048 / Rrim(I) all: 0.134 / Rsym value: 0.122 / Net I/σ(I): 10.4
Reflection shellResolution: 2.1→2.23 Å / Redundancy: 3.83 % / CC1/2: 0.555 / Rpim(I) all: 0.247 / Rrim(I) all: 1.065 / Rsym value: 0.896 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2CB2

2cb2


Resolution: 2.102→76.9 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.77
RfactorNum. reflection% reflection
Rfree0.2118 2499 2.18 %
Rwork0.1641 --
obs0.1651 114883 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.102→76.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14822 0 7 811 15640
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00815429
X-RAY DIFFRACTIONf_angle_d0.92520898
X-RAY DIFFRACTIONf_dihedral_angle_d16.1329240
X-RAY DIFFRACTIONf_chiral_restr0.0542170
X-RAY DIFFRACTIONf_plane_restr0.0062693
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1015-2.14190.30431460.25886158X-RAY DIFFRACTION99
2.1419-2.18560.29771260.23176226X-RAY DIFFRACTION100
2.1856-2.23320.31891370.25816227X-RAY DIFFRACTION100
2.2332-2.28510.4031320.33386184X-RAY DIFFRACTION99
2.2851-2.34230.2421410.20176237X-RAY DIFFRACTION100
2.3423-2.40560.28971420.19646183X-RAY DIFFRACTION100
2.4056-2.47640.25881370.18486281X-RAY DIFFRACTION100
2.4764-2.55630.24391320.17136243X-RAY DIFFRACTION100
2.5563-2.64770.22031450.1696224X-RAY DIFFRACTION100
2.6477-2.75370.24991330.17286274X-RAY DIFFRACTION100
2.7537-2.87910.21181530.16016224X-RAY DIFFRACTION100
2.8791-3.03080.19781390.15966211X-RAY DIFFRACTION100
3.0308-3.22070.19151290.15956307X-RAY DIFFRACTION100
3.2207-3.46940.22531440.14926222X-RAY DIFFRACTION100
3.4694-3.81850.16761410.14216272X-RAY DIFFRACTION100
3.8185-4.37110.15171320.12716278X-RAY DIFFRACTION100
4.3711-5.50690.17771400.12846288X-RAY DIFFRACTION100
5.5069-76.98160.19021500.16376345X-RAY DIFFRACTION100

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