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- PDB-3t2y: Crystal structure of sulfide:quinone oxidoreductase His132Ala var... -

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Basic information

Entry
Database: PDB / ID: 3t2y
TitleCrystal structure of sulfide:quinone oxidoreductase His132Ala variant from Acidithiobacillus ferrooxidans with bound disulfide
ComponentsSulfide-quinone reductase, putative
KeywordsOXIDOREDUCTASE / sulfide:quinone oxidoreductase / His132Ala variant / integral monotopic membrane protein / complex with disulfide
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
FLAVIN-ADENINE DINUCLEOTIDE / HYDROSULFURIC ACID / Hydrogen disulfide / Sulfide-quinone reductase
Similarity search - Component
Biological speciesAcidithiobacillus ferrooxidans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / refinement / Resolution: 2.5001 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 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2012Group: Database references
Revision 1.2Mar 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 / 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_leaving_atom_flag / _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)48,7945
Polymers47,3981
Non-polymers1,3964
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)150.070, 150.070, 81.860
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 / Sugars , 2 types, 2 molecules A

#1: Protein Sulfide-quinone reductase, putative


Mass: 47397.570 Da / Num. of mol.: 1 / Mutation: H132A
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 , 4 types, 72 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-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE


Mass: 34.081 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2S
#5: Chemical ChemComp-S2H / Hydrogen disulfide


Mass: 66.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2S2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.81 Å3/Da / Density % sol: 56.18 %
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, 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: 2.5→50.9 Å / Num. all: 19125 / Num. obs: 15185 / % possible obs: 79.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10 % / Biso Wilson estimate: 51.4 Å2 / Rmerge(I) obs: 0.123 / Rsym value: 0.123 / Net I/σ(I): 14.1
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.893 / Mean I/σ(I) obs: 2.4 / Num. unique all: 2733 / Rsym value: 0.893 / % possible all: 89.2

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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: 2.5001→49.122 Å / SU ML: 0.98 / σ(F): 1.35 / Phase error: 26.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2634 1434 5.09 %random
Rwork0.1775 ---
obs0.1817 15185 78.86 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.434 Å2 / ksol: 0.327 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.1626 Å2-0 Å20 Å2
2---7.1626 Å2-0 Å2
3---14.3251 Å2
Refinement stepCycle: LAST / Resolution: 2.5001→49.122 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3096 0 91 69 3256
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073277
X-RAY DIFFRACTIONf_angle_d1.0784442
X-RAY DIFFRACTIONf_dihedral_angle_d16.0781197
X-RAY DIFFRACTIONf_chiral_restr0.07485
X-RAY DIFFRACTIONf_plane_restr0.008561
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.58940.39771790.33012983X-RAY DIFFRACTION89
2.5894-2.69310.36781110.29661866X-RAY DIFFRACTION56
2.6931-2.81560.32981560.24622990X-RAY DIFFRACTION88
2.8156-2.96410.3312020.21922936X-RAY DIFFRACTION88
2.9641-3.14970.2871510.19992953X-RAY DIFFRACTION87
3.1497-3.39290.26821380.17652959X-RAY DIFFRACTION87
3.3929-3.73420.27781130.16441905X-RAY DIFFRACTION56
3.7342-4.27430.21861290.15462421X-RAY DIFFRACTION71
4.2743-5.38410.17221440.11392856X-RAY DIFFRACTION84
5.3841-49.13130.25591110.16742843X-RAY DIFFRACTION82
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)
12.37880.4737-0.32012.6602-0.48810.31290.1216-0.46140.21240.4978-0.20310.20430.0514-0.20680.04550.3141-0.11110.08590.404-0.03410.184740.6002-26.850212.2142
21.827-0.15590.15562.38210.02641.13760.1355-0.11790.02020.3941-0.3064-1.6735-0.52830.16980.00640.1604-0.1635-0.17290.19580.11210.52264.4705-17.05696.1098
33.13660.70530.41772.1959-0.74360.1187-0.04130.297-0.3016-0.16610.089-0.05760.1346-0.1336-0.03290.2121-0.05620.04650.339-0.03260.138345.7974-25.9311-2.5443
42.35250.3983-1.81673.0459-1.01581.47660.01570.39190.0884-0.23730.1380.14610.0114-0.3945-0.09930.2472-0.0540.03390.18440.00970.33943.5019-10.4256-1.9901
53.20422.2254-2.33452.8427-1.60283.25820.353-0.29980.68910.8188-0.1190.6036-0.1023-0.2276-0.15780.4574-0.02750.12990.3194-0.06610.367743.2386-7.197611.8781
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 378:407)

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