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- PDB-3t0k: Crystal structure of sulfide:quinone oxidoreductase from Acidithi... -

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Basic information

Entry
Database: PDB / ID: 3t0k
TitleCrystal structure of sulfide:quinone oxidoreductase from Acidithiobacillus ferrooxidans with bound trisulfide and decylubiquinone
ComponentsSulfide-quinone reductase, putative
KeywordsOXIDOREDUCTASE / sulfide:quinone oxidoreductase / integral monotopic membrane protein / complex with tetrasulfur and decylubiquinone
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 / trisulfane / Sulfide-quinone reductase
Similarity search - Component
Biological speciesAcidithiobacillus ferrooxidans ATCC 23270 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / refinement / Resolution: 2 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 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2012Group: Database references
Revision 1.2May 7, 2014Group: 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 / 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)49,2059
Polymers47,7661
Non-polymers1,4398
Water3,963220
1
A: Sulfide-quinone reductase, putative
hetero molecules

A: Sulfide-quinone reductase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,40918
Polymers95,5322
Non-polymers2,87716
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area5890 Å2
ΔGint-87 kcal/mol
Surface area32840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.960, 149.960, 82.050
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

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Protein , 1 types, 1 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 ATCC 23270 (bacteria)
Strain: ATCC 23270 / DSM 14882 / NCIB 8455 / Gene: AFE_1792 / Production host: Escherichia coli (E. coli) / References: UniProt: B7JBP8

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Non-polymers , 6 types, 228 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
#3: 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
#4: Chemical ChemComp-S3H / trisulfane


Mass: 98.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2S3
#5: Chemical
ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE


Mass: 34.081 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H2S
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.79 Å3/Da / Density % sol: 55.88 %
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, 5 mM decylubiquinone, 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 9, 2011
RadiationMonochromator: ACCEL/BRUKER double crystal monochromator (DCM)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2→50.9 Å / Num. all: 37192 / Num. obs: 33510 / % possible obs: 90.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.6 % / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/σ(I): 13
Reflection shellResolution: 2→2.11 Å / Redundancy: 14.7 % / Rmerge(I) obs: 1.022 / Mean I/σ(I) obs: 2.9 / Rsym value: 1.022 / % possible all: 82.1

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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→39.12 Å / SU ML: 0.6 / σ(F): 1.34 / Phase error: 23.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2276 3146 5.01 %
Rwork0.18 --
obs0.1823 33510 90.06 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.295 Å2 / ksol: 0.331 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.6422 Å20 Å20 Å2
2---5.6422 Å2-0 Å2
3---11.2845 Å2
Refinement stepCycle: LAST / Resolution: 2→39.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3222 0 88 220 3530
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073400
X-RAY DIFFRACTIONf_angle_d1.1924611
X-RAY DIFFRACTIONf_dihedral_angle_d14.5471252
X-RAY DIFFRACTIONf_chiral_restr0.076491
X-RAY DIFFRACTIONf_plane_restr0.005585
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.03130.37141810.32793000X-RAY DIFFRACTION100
2.0313-2.06460.35361540.30772984X-RAY DIFFRACTION100
2.0646-2.10020.217730.25141274X-RAY DIFFRACTION42
2.1002-2.13840.2841530.2393053X-RAY DIFFRACTION100
2.1384-2.17950.25321470.23033016X-RAY DIFFRACTION100
2.1795-2.2240.29081440.20633020X-RAY DIFFRACTION100
2.224-2.27230.2629390.20861176X-RAY DIFFRACTION38
2.2723-2.32520.21561530.1942997X-RAY DIFFRACTION100
2.3252-2.38330.22671590.20363034X-RAY DIFFRACTION100
2.3833-2.44770.2631900.20392955X-RAY DIFFRACTION100
2.4477-2.51980.24061340.19263034X-RAY DIFFRACTION100
2.5198-2.60110.24871740.20852996X-RAY DIFFRACTION100
2.6011-2.6940.31421050.21231779X-RAY DIFFRACTION59
2.694-2.80180.27171720.19993014X-RAY DIFFRACTION100
2.8018-2.92930.21981750.192998X-RAY DIFFRACTION100
2.9293-3.08370.26031410.19553013X-RAY DIFFRACTION100
3.0837-3.27680.24131550.19933046X-RAY DIFFRACTION100
3.2768-3.52970.22261430.18222430X-RAY DIFFRACTION82
3.5297-3.88460.19061150.16832211X-RAY DIFFRACTION78
3.8846-4.4460.20211130.14122656X-RAY DIFFRACTION100
4.446-5.59890.17991500.13263023X-RAY DIFFRACTION100
5.5989-39.12720.22061760.17912975X-RAY DIFFRACTION99
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)
12.11690.54550.05143.2596-0.5370.97230.0814-0.2856-0.15910.4934-0.0914-0.0454-0.0033-0.26020.01140.3405-0.10340.00770.42920.06160.188240.6203-26.593912.2324
20.9527-0.23680.06562.3391-0.13810.0890.15320.03290.17470.441-0.5018-2.1514-0.28450.528-0.0221-0.0301-0.3834-0.11610.13460.2030.939164.4343-17.1186.1475
31.90480.7010.10833.3305-0.89811.0312-0.01420.2315-0.086-0.36250.0154-0.38960.2258-0.1382-0.02250.3175-0.06940.0520.40050.0120.226745.7516-25.8621-2.5242
41.48870.0387-0.54742.6701-0.92890.89380.03730.02190.1078-0.13950.11880.15770.1318-0.5146-0.17490.3355-0.0790.03990.40120.04640.26843.7116-10.3374-1.9742
51.81341.1046-1.58332.4057-1.20182.5249-0.02240.10610.35530.48270.11380.2954-0.1104-0.5447-0.02250.38360.03470.06780.4007-0.00240.357542.17-7.212411.4226
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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