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

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Basic information

Entry
Database: PDB / ID: 3szc
TitleCrystal structure of sulfide:quinone oxidoreductase from Acidithiobacillus ferrooxidans in complex with gold (I) cyanide
ComponentsSulfide-quinone reductase, putative
KeywordsOXIDOREDUCTASE / sulfide:quinone oxidoreductase / integral monotopic membrane protein / complex with gold (I) cyanide
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 / refinement / Resolution: 2.2 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 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2012Group: Database references
Revision 1.2Mar 27, 2013Group: 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_struct_conn_angle / struct_conn / struct_conn_type / 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 / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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_type.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)49,66310
Polymers47,7661
Non-polymers1,8979
Water1,51384
1
A: Sulfide-quinone reductase, putative
hetero molecules

A: Sulfide-quinone reductase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,32620
Polymers95,5322
Non-polymers3,79418
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area1640 Å2
ΔGint-9 kcal/mol
Surface area34330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.540, 149.540, 81.740
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 (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, 93 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-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Au
#5: Chemical ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE


Mass: 34.081 Da / Num. of mol.: 3 / 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.: 84 / 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: 2.76 Å3/Da / Density % sol: 55.46 %
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 10, 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: 2.2→50.8 Å / Num. all: 27902 / Num. obs: 25168 / % possible obs: 90.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.4 % / Biso Wilson estimate: 47.46 Å2 / Rmerge(I) obs: 0.14 / Rsym value: 0.14 / Net I/σ(I): 10.5
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 14.2 % / Rmerge(I) obs: 1.573 / Mean I/σ(I) obs: 1.9 / Num. unique all: 3990 / Rsym value: 1.573 / % possible all: 74.3

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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: 2.2→48.948 Å / SU ML: 0.8 / σ(F): 1.35 / Phase error: 24.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2244 2373 5.06 %random
Rwork0.1814 ---
obs0.1836 25168 90.23 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.557 Å2 / ksol: 0.343 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.3417 Å20 Å20 Å2
2---2.3417 Å2-0 Å2
3---4.6835 Å2
Refinement stepCycle: LAST / Resolution: 2.2→48.948 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3222 0 87 84 3393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013395
X-RAY DIFFRACTIONf_angle_d1.2454596
X-RAY DIFFRACTIONf_dihedral_angle_d15.0211247
X-RAY DIFFRACTIONf_chiral_restr0.08489
X-RAY DIFFRACTIONf_plane_restr0.008583
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.24490.43361160.34082308X-RAY DIFFRACTION100
2.2449-2.29370.3641830.31821654X-RAY DIFFRACTION100
2.2937-2.34710.32171450.29412899X-RAY DIFFRACTION100
2.3471-2.40580.34711470.28942946X-RAY DIFFRACTION100
2.4058-2.47080.33461710.28932875X-RAY DIFFRACTION100
2.4708-2.54350.3151430.2582920X-RAY DIFFRACTION100
2.5435-2.62560.31441570.2472891X-RAY DIFFRACTION100
2.6256-2.71950.2871870.23981645X-RAY DIFFRACTION57
2.7195-2.82830.30221730.22362878X-RAY DIFFRACTION100
2.8283-2.9570.27651570.21922871X-RAY DIFFRACTION100
2.957-3.11290.29021690.19782908X-RAY DIFFRACTION100
3.1129-3.30790.2981490.19752896X-RAY DIFFRACTION100
3.3079-3.56320.20261350.18172368X-RAY DIFFRACTION81
3.5632-3.92170.22021250.15911815X-RAY DIFFRACTION75
3.9217-4.48880.1691380.12722793X-RAY DIFFRACTION100
4.4888-5.65410.14011530.12242898X-RAY DIFFRACTION100
5.6541-48.96050.14841250.15762942X-RAY DIFFRACTION100
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)
16.1110.83030.13113.5595-0.11111.60870.0795-0.6116-0.24680.5479-0.07220.08850.0582-0.3507-0.01650.3646-0.07090.04820.40820.06720.253540.4783-26.710612.2163
24.498-0.88570.48582.8982-0.98583.0918-0.0515-0.11230.33030.415-0.2189-1.221-0.40030.51640.25510.323-0.0976-0.09180.35260.03810.766664.3023-17.14756.2743
37.32370.23690.74933.2357-0.42021.79180.0820.52470.0254-0.2661-0.0461-0.27520.1401-0.0638-0.03590.2685-0.0520.06780.30740.00110.225145.6734-25.8464-2.5561
44.9941.4733-0.81315.9285-0.53343.0975-0.12690.2773-0.003-0.22280.1774-0.0320.1289-0.4236-0.04440.2527-0.02090.03520.24250.02520.312143.5478-10.2527-2.0577
56.67435.9246-5.97656.9048-5.29068.79130.1599-0.0011.06430.4030.01170.9595-0.1926-0.8423-0.17130.37150.04560.05270.3499-0.08640.521842.0423-7.224111.4795
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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