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- PDB-3sz0: Crystal structure of sulfide:quinone oxidoreductase from Acidithi... -

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Basic information

Entry
Database: PDB / ID: 3sz0
TitleCrystal structure of sulfide:quinone oxidoreductase from Acidithiobacillus ferrooxidans in complex with sodium selenide
ComponentsSulfide-quinone reductase, putative
KeywordsOXIDOREDUCTASE / sulfide:quinone oxidoreductase / integral monotopic membrane protein / complex with selenide
Function / homology
Function and homology information


bacterial sulfide:quinone reductase / sulfide:quinone oxidoreductase activity / aerobic electron transport chain / NAD(P)H dehydrogenase (quinone) activity / quinone binding / nucleotide binding / membrane
Similarity search - Function
: / FAD/NAD(P)-binding domain - #100 / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
triselane / FLAVIN-ADENINE DINUCLEOTIDE / SELENIUM ATOM / Sulfide-quinone reductase
Similarity search - Component
Biological speciesAcidithiobacillus ferrooxidans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / refinement / Resolution: 2.1501 Å
AuthorsCherney, M.M. / Zhang, Y. / James, M.N.G. / Weiner, J.H.
CitationJournal: J.Struct.Biol. / Year: 2012
Title: Structure-activity characterization of sulfide:quinone oxidoreductase variants.
Authors: Cherney, M.M. / Zhang, Y. / James, M.N. / Weiner, J.H.
History
DepositionJul 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2012Group: Database references
Revision 1.2Jul 25, 2012Group: Other
Revision 1.3Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_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_ref_seq_dif.details / _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: Sulfide-quinone reductase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5557
Polymers47,7661
Non-polymers1,7896
Water4,053225
1
A: Sulfide-quinone reductase, putative
hetero molecules

A: Sulfide-quinone reductase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,11014
Polymers95,5322
Non-polymers3,57812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area1760 Å2
ΔGint-10 kcal/mol
Surface area34220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.900, 149.900, 81.890
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-804-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Sulfide-quinone reductase, putative


Mass: 47765.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidithiobacillus ferrooxidans (bacteria)
Strain: ATCC 23270 / DSM 14882 / NCIB 8455 / Gene: AFE_1792 / Production host: Escherichia coli (E. coli) / References: UniProt: B7JBP8
#3: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 5 types, 230 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-6SE / triselane


Mass: 238.896 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2Se3
#6: Chemical ChemComp-SE / SELENIUM ATOM


Mass: 78.960 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Se
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.78 Å3/Da / Density % sol: 55.76 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 30% PEG 600, 0.1 M bis-tris buffer, 0.1 M MgSO4, 0.05% DDM, 2 mM Na2Se, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 10, 2011
RadiationMonochromator: ACCEL/BRUKER double crystal monochromator (DCM), featuring indirectly cryo-cooled first crystal and sagittally focusing second crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.15→49.1 Å / Num. all: 29907 / Num. obs: 27066 / % possible obs: 90.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.2 % / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 14.1
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.923 / Mean I/σ(I) obs: 2.9 / Rsym value: 0.923 / % possible all: 76.1

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX(phenix.refine: 1.7.1_743)model building
PHENIX(phenix.refine: 1.7.1_743)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIX1.7.1_743phasing
RefinementMethod to determine structure: refinement / Resolution: 2.1501→43.272 Å / SU ML: 0.69 / σ(F): 1.34 / Phase error: 22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2178 1378 5.09 %
Rwork0.1692 --
obs0.1717 27006 90.42 %
all-25732 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.273 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.7802 Å2-0 Å20 Å2
2---3.7802 Å2-0 Å2
3---7.5604 Å2
Refinement stepCycle: LAST / Resolution: 2.1501→43.272 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3222 0 98 225 3545
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083405
X-RAY DIFFRACTIONf_angle_d1.1974615
X-RAY DIFFRACTIONf_dihedral_angle_d16.5241269
X-RAY DIFFRACTIONf_chiral_restr0.076492
X-RAY DIFFRACTIONf_plane_restr0.008583
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1501-2.19140.32811590.25892963X-RAY DIFFRACTION100
2.1914-2.23610.27841410.23212893X-RAY DIFFRACTION100
2.2361-2.28480.3065610.21661163X-RAY DIFFRACTION100
2.2848-2.33790.24861480.21312988X-RAY DIFFRACTION100
2.3379-2.39640.27551600.20462909X-RAY DIFFRACTION100
2.3964-2.46120.30191610.22392939X-RAY DIFFRACTION100
2.4612-2.53360.28571420.20652969X-RAY DIFFRACTION100
2.5336-2.61530.30651610.20392946X-RAY DIFFRACTION100
2.6153-2.70880.2437850.19491700X-RAY DIFFRACTION57
2.7088-2.81720.30831470.2072943X-RAY DIFFRACTION100
2.8172-2.94540.25961380.18112956X-RAY DIFFRACTION99
2.9454-3.10070.23441730.182923X-RAY DIFFRACTION100
3.1007-3.29490.24561900.16492899X-RAY DIFFRACTION99
3.2949-3.54920.22761100.16122418X-RAY DIFFRACTION81
3.5492-3.90610.15641270.15091987X-RAY DIFFRACTION77
3.9061-4.47080.16431650.12642669X-RAY DIFFRACTION99
4.4708-5.63080.16441680.12282906X-RAY DIFFRACTION98
5.6308-43.28110.19821410.16942917X-RAY DIFFRACTION98
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)
12.38731.1629-0.43552.7712-0.93651.15850.0987-0.3274-0.03320.5151-0.11340.0272-0.0462-0.18230.01610.2648-0.07630.02080.31770.01970.144440.6105-26.781112.2407
22.3460.1023-0.24572.1282-0.23430.41490.2219-0.2482-0.03180.2721-0.4797-1.5199-0.07410.22410.12650.2174-0.1082-0.16180.26920.1280.619464.3751-17.06716.1315
33.13471.21860.09012.5784-0.62190.99280.0270.2239-0.0817-0.26410.0246-0.23490.1721-0.1526-0.04230.2177-0.04610.04180.29570.01960.155845.7898-25.9127-2.5391
44.79341.9887-0.4274.1173-0.39991.26330.12930.02970.2792-0.16160.14010.2398-0.088-0.6416-0.10960.1881-0.00480.05280.26910.05780.228843.543-10.2972-2.0102
54.77733.0925-4.00353.0003-2.57633.50530.23610.13190.98850.6610.09110.61120.0034-0.3754-0.30890.38640.0140.14820.2794-0.01470.342441.9633-7.410111.4633
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:161)
2X-RAY DIFFRACTION2chain 'A' and (resseq 162:232)
3X-RAY DIFFRACTION3chain 'A' and (resseq 233:341)
4X-RAY DIFFRACTION4chain 'A' and (resseq 342:377)
5X-RAY DIFFRACTION5chain 'A' and (resseq 378:410)

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