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- PDB-3sxi: Crystal structure of sulfide:quinone oxidoreductase Cys128Ala var... -

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Basic information

Entry
Database: PDB / ID: 3sxi
TitleCrystal structure of sulfide:quinone oxidoreductase Cys128Ala variant from Acidithiobacillus ferrooxidans complexed with decylubiquinone
ComponentsSulfide-quinone reductase, putative
KeywordsOXIDOREDUCTASE / sulfide:quinone oxidoreductase / Cys128Ala variant / integral monotopic membrane protein / complex with sulfide
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
Chem-DCQ / FLAVIN-ADENINE DINUCLEOTIDE / HYDROSULFURIC ACID / Sulfide-quinone reductase
Similarity search - Component
Biological speciesAcidithiobacillus ferrooxidans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1792 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 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
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_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.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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)49,5859
Polymers47,7341
Non-polymers1,8518
Water4,954275
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A: Sulfide-quinone reductase, putative
hetero molecules

A: Sulfide-quinone reductase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,17018
Polymers95,4682
Non-polymers3,70216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area1730 Å2
ΔGint-10 kcal/mol
Surface area34450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.090, 150.090, 81.460
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-659-

HOH

21A-708-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Sulfide-quinone reductase, putative


Mass: 47733.895 Da / Num. of mol.: 1 / Mutation: C128A
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, 282 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-DCQ / 2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione / decylubiquinone


Mass: 322.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H30O4
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE


Mass: 34.081 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H2S
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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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: 2.77 Å3/Da / Density % sol: 55.67 %
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, 2mM decylubiquinone, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 28, 2009
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.1792→50 Å / Num. all: 28719 / Num. obs: 28461 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.8 % / Biso Wilson estimate: 33.44 Å2 / Rmerge(I) obs: 0.115 / Rsym value: 0.115 / Net I/σ(I): 22.1
Reflection shellResolution: 2.1792→2.26 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.889 / Mean I/σ(I) obs: 2.04 / Num. unique all: 2815 / Rsym value: 0.889 / % possible all: 97.7

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIX(phenix.refine: 1.7_650)model building
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.7_650phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.1792→49.128 Å / SU ML: 0.3 / σ(F): 1.33 / Phase error: 21.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2195 1441 5.06 %Random
Rwork0.1668 ---
obs0.1695 28457 99.04 %-
all-28744 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.769 Å2 / ksol: 0.347 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.7525 Å2-0 Å20 Å2
2---2.7525 Å2-0 Å2
3---5.505 Å2
Refinement stepCycle: LAST / Resolution: 2.1792→49.128 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3221 0 120 275 3616
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083437
X-RAY DIFFRACTIONf_angle_d1.1564660
X-RAY DIFFRACTIONf_dihedral_angle_d20.9391303
X-RAY DIFFRACTIONf_chiral_restr0.075502
X-RAY DIFFRACTIONf_plane_restr0.008586
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1792-2.25710.30391420.23612579X-RAY DIFFRACTION97
2.2571-2.34740.29371310.21472674X-RAY DIFFRACTION99
2.3474-2.45430.30821490.21022668X-RAY DIFFRACTION100
2.4543-2.58370.28121440.20062673X-RAY DIFFRACTION100
2.5837-2.74550.24451440.19182685X-RAY DIFFRACTION100
2.7455-2.95750.26861530.17562695X-RAY DIFFRACTION100
2.9575-3.2550.2411440.17262697X-RAY DIFFRACTION99
3.255-3.72590.19071440.16412715X-RAY DIFFRACTION99
3.7259-4.69370.17811630.12592728X-RAY DIFFRACTION99
4.6937-49.14090.171270.15222902X-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)
10.36360.3361-0.18761.0431-0.35950.60760.0037-0.0171-0.07530.1712-0.01110.08810.0729-0.1825-0.0240.1451-0.0530.01220.20920.02180.151140.7155-26.734912.2424
20.4127-0.04870.02410.2952-0.03970.07290.1255-0.0346-0.02740.0081-0.2054-0.6171-0.08090.0880.01180.1283-0.0644-0.0510.1740.05770.364664.5484-17.13866.2484
30.39130.5065-0.28810.8541-0.41390.2465-0.02020.16450.0218-0.1530.0401-0.09970.1969-0.1260.04110.1519-0.04610.0070.22260.00450.14945.7749-25.7842-2.4877
40.29550.07290.02510.8588-0.21560.2470.0217-0.0550.0951-0.180.14240.0388-0.0023-0.2476-0.08840.1901-0.03990.01730.24680.04610.210543.6565-10.2766-1.9477
51.0812-0.083-0.18290.4146-0.02560.56610.03020.03490.48030.20210.12840.0974-0.0781-0.1688-0.06420.189-0.01280.05290.19160.00610.187342.1677-7.256911.6273
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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