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- PDB-6qo0: I47W mutated sulfur oxygenase reductase from Acidianus ambivaens -

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Basic information

Entry
Database: PDB / ID: 6qo0
TitleI47W mutated sulfur oxygenase reductase from Acidianus ambivaens
ComponentsSulfur oxygenase/reductase
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 / MOLECULAR REPLACEMENT / Resolution: 1.65 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
DepositionFeb 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sulfur oxygenase/reductase
B: Sulfur oxygenase/reductase
C: Sulfur oxygenase/reductase
D: Sulfur oxygenase/reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,0398
Polymers145,8164
Non-polymers2234
Water17,853991
1
A: Sulfur oxygenase/reductase
B: Sulfur oxygenase/reductase
C: Sulfur oxygenase/reductase
D: Sulfur oxygenase/reductase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)876,23648
Polymers874,89624
Non-polymers1,34024
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_785-y+2,x-y+3,z1
crystal symmetry operation3_475-x+y-1,-x+2,z1
crystal symmetry operation10_777-y+2,-x+2,-z+5/21
crystal symmetry operation11_457-x+y-1,y,-z+5/21
crystal symmetry operation12_587x,x-y+3,-z+5/21
Buried area137590 Å2
ΔGint-1150 kcal/mol
Surface area209000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.160, 158.160, 227.640
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11D-715-

HOH

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Components

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


Mass: 36453.988 Da / Num. of mol.: 4 / Mutation: I47W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidianus ambivalens (archaea) / Gene: sor / Production host: Escherichia coli (E. coli) / References: UniProt: P29082, sulfur oxygenase/reductase
#2: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 991 / 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: 2.92 Å3/Da / Density % sol: 57.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.2 / Details: 0.1 sodium acetate pH 4.2, 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: 1.65→113.8 Å / Num. obs: 199561 / % possible obs: 99.7 % / Redundancy: 59.4 % / Biso Wilson estimate: 33 Å2 / CC1/2: 1 / Rpim(I) all: 0.157 / Rrim(I) all: 0.148 / Rsym value: 0.147 / Net I/σ(I): 29.2
Reflection shellResolution: 1.65→1.69 Å / Redundancy: 56.8 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 14480 / CC1/2: 0.621 / Rpim(I) all: 0.1332 / Rrim(I) all: 4.272 / Rsym value: 4.234 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→113.8 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.34
RfactorNum. reflection% reflection
Rfree0.191 3200 1.6 %
Rwork0.1676 --
obs0.168 199485 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.65→113.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9887 0 4 991 10882
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610344
X-RAY DIFFRACTIONf_angle_d0.84814025
X-RAY DIFFRACTIONf_dihedral_angle_d15.8376181
X-RAY DIFFRACTIONf_chiral_restr0.0551459
X-RAY DIFFRACTIONf_plane_restr0.0061802
Refinement TLS params.Method: refined / Origin x: -98.7971 Å / Origin y: 194.2093 Å / Origin z: 256.6346 Å
111213212223313233
T0.2483 Å2-0.0484 Å2-0.0022 Å2-0.2306 Å2-0.0144 Å2--0.2335 Å2
L0.0792 °2-0.0152 °20.008 °2-0.0692 °2-0.0042 °2--0.2286 °2
S-0.0074 Å °0.0146 Å °-0.0326 Å °-0.0168 Å °-0.0009 Å °0.0215 Å °0.122 Å °-0.0681 Å °0.0083 Å °
Refinement TLS groupSelection details: all

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