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- PDB-6qka: Di-tert-butyl Polysulfide inhibited sulfur oxygenase reductase -

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Basic information

Entry
Database: PDB / ID: 6qka
TitleDi-tert-butyl Polysulfide inhibited sulfur oxygenase reductase
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 / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsFrazao, C. / Klezin, A. / Poell, U.
Funding support Portugal, Germany, 2items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a TecnologiaLIOA-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 28, 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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
Revision 1.2Oct 9, 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)219,39012
Polymers219,0556
Non-polymers3356
Water13,745763
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)877,56148
Polymers876,22124
Non-polymers1,34024
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 area137620 Å2
ΔGint-1133 kcal/mol
Surface area207950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.913, 161.913, 153.901
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: 36509.195 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: RESIDUES CYS_31 APPEAR DERIVATIZED INTO TSY_31, RESIDUES CYS_101 APEAR 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
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 763 / 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: 46.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1 M sodium citrate pH 5.6, 1 M ammonium phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.85001 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.85001 Å / Relative weight: 1
ReflectionResolution: 2.1→111.5 Å / Num. obs: 227941 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 33 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.041 / Rrim(I) all: 0.168 / Rsym value: 0.154 / Net I/σ(I): 10.4
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 1.44 / CC1/2: 0.552 / Rpim(I) all: 0.2166 / Rrim(I) all: 1.778 / Rsym value: 1.071 / % possible all: 99.6

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Processing

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

2cb2


Resolution: 2.1→76.951 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.28 / Phase error: 21.28
RfactorNum. reflection% reflectionSelection details
Rfree0.2033 4484 1.97 %thin resolution shells
Rwork0.1626 ---
obs0.1634 227895 99.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→76.951 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14820 0 6 763 15589
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00815258
X-RAY DIFFRACTIONf_angle_d0.91120676
X-RAY DIFFRACTIONf_dihedral_angle_d15.2679102
X-RAY DIFFRACTIONf_chiral_restr0.0542154
X-RAY DIFFRACTIONf_plane_restr0.0062658
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1001-2.1240.3371430.32467318X-RAY DIFFRACTION98
2.124-2.14890.37111560.29447429X-RAY DIFFRACTION100
2.1489-2.17520.27051610.26547379X-RAY DIFFRACTION100
2.1752-2.20270.32781250.25817529X-RAY DIFFRACTION100
2.2027-2.23170.28481600.24947452X-RAY DIFFRACTION100
2.2317-2.26220.2891660.25117458X-RAY DIFFRACTION100
2.2622-2.29460.29131540.23787426X-RAY DIFFRACTION100
2.2946-2.32880.28291520.22457457X-RAY DIFFRACTION100
2.3288-2.36520.27121620.22257443X-RAY DIFFRACTION100
2.3652-2.4040.24151480.22557434X-RAY DIFFRACTION100
2.404-2.44540.23911240.22187476X-RAY DIFFRACTION100
2.4454-2.48990.25121480.21557440X-RAY DIFFRACTION100
2.4899-2.53780.2651660.19787469X-RAY DIFFRACTION100
2.5378-2.58960.27221700.19537371X-RAY DIFFRACTION100
2.5896-2.64590.2251160.18677538X-RAY DIFFRACTION100
2.6459-2.70750.26771440.18377456X-RAY DIFFRACTION100
2.7075-2.77520.19541740.16917347X-RAY DIFFRACTION100
2.7752-2.85020.18971730.15877508X-RAY DIFFRACTION100
2.8502-2.93410.2119900.15547575X-RAY DIFFRACTION100
2.9341-3.02880.20521700.15557340X-RAY DIFFRACTION100
3.0288-3.13710.22951360.167544X-RAY DIFFRACTION100
3.1371-3.26270.19111660.14947410X-RAY DIFFRACTION100
3.2627-3.41120.18281300.14147418X-RAY DIFFRACTION100
3.4112-3.5910.22481300.13917514X-RAY DIFFRACTION100
3.591-3.8160.18431330.13197483X-RAY DIFFRACTION100
3.816-4.11060.1462160.12157347X-RAY DIFFRACTION100
4.1106-4.52420.12812100.10997428X-RAY DIFFRACTION100
4.5242-5.17880.2624160.11127576X-RAY DIFFRACTION100
5.1788-6.52420.18441550.1537450X-RAY DIFFRACTION100
6.5242-77.00220.15541900.14587396X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 45.9969 Å / Origin y: 100.5021 Å / Origin z: 77.7495 Å
111213212223313233
T0.2212 Å20.0119 Å20.001 Å2-0.2244 Å20.0095 Å2--0.2345 Å2
L0.0447 °20.0018 °2-0.0086 °2-0.0604 °20.009 °2--0.0468 °2
S0.0067 Å °0.0014 Å °0.0117 Å °0.0019 Å °0.0014 Å °0.0266 Å °-0.011 Å °-0.0242 Å °-0 Å °
Refinement TLS groupSelection details: all

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