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- PDB-3szf: Crystal structure of sulfide:quinone oxidoreductase H198A variant... -

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Basic information

Entry
Database: PDB / ID: 3szf
TitleCrystal structure of sulfide:quinone oxidoreductase H198A variant from Acidithiobacillus ferrooxidans in complex with bound trisulfide and decylubiquinone
ComponentsSulfide-quinone reductase, putative
KeywordsOXIDOREDUCTASE / sulfide:quinone oxidoreductase / His198Ala variant / integral monotopic membrane protein / complex with tetrasulfide and ubiquinone
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / refinement / Resolution: 2.0994 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 1.2May 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 / 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)49,64810
Polymers47,6991
Non-polymers1,9499
Water5,026279
1
A: Sulfide-quinone reductase, putative
hetero molecules

A: Sulfide-quinone reductase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,29620
Polymers95,3982
Non-polymers3,89818
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area1710 Å2
ΔGint-11 kcal/mol
Surface area34730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.234, 150.234, 81.891
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-876-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Sulfide-quinone reductase, putative


Mass: 47698.891 Da / Num. of mol.: 1 / Fragment: Sulfide:quinone oxidoreductase / Mutation: H198A
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 , 6 types, 287 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-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE


Mass: 34.081 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H2S
#6: Chemical ChemComp-S3H / trisulfane


Mass: 98.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2S3
#7: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 279 / 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: 2.8 Å3/Da / Density % sol: 56.02 %
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: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 10, 2010
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: 2.099→50 Å / Num. all: 32310 / Num. obs: 30889 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 18.7
Reflection shellResolution: 2.099→2.18 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.642 / Mean I/σ(I) obs: 1.5 / Rsym value: 0.642 / % possible all: 73.7

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.7.1_743) / Classification: refinement
RefinementMethod to determine structure: refinement / Resolution: 2.0994→43.369 Å / SU ML: 0.66 / σ(F): 1.34 / Phase error: 22.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2328 1565 5.08 %
Rwork0.18 --
obs0.1827 30818 95.49 %
all-32270 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.191 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.8686 Å2-0 Å20 Å2
2---0.8686 Å2-0 Å2
3---1.7373 Å2
Refinement stepCycle: LAST / Resolution: 2.0994→43.369 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3217 0 123 279 3619
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083427
X-RAY DIFFRACTIONf_angle_d1.1974644
X-RAY DIFFRACTIONf_dihedral_angle_d16.3731284
X-RAY DIFFRACTIONf_chiral_restr0.072493
X-RAY DIFFRACTIONf_plane_restr0.008584
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0994-2.16710.30341150.23971972X-RAY DIFFRACTION73
2.1671-2.24460.34741250.2542269X-RAY DIFFRACTION83
2.2446-2.33440.30821220.24712585X-RAY DIFFRACTION94
2.3344-2.44070.25841540.18862741X-RAY DIFFRACTION100
2.4407-2.56930.25641440.18672735X-RAY DIFFRACTION100
2.5693-2.73030.26251520.19682768X-RAY DIFFRACTION100
2.7303-2.94110.28071740.19642739X-RAY DIFFRACTION100
2.9411-3.23690.24691430.18112772X-RAY DIFFRACTION100
3.2369-3.70510.23351400.17752821X-RAY DIFFRACTION100
3.7051-4.66720.16481500.1382835X-RAY DIFFRACTION100
4.6672-43.37810.20011460.16973016X-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)
11.60420.40240.02421.1142-0.13920.60250.0052-0.1835-0.06640.1734-0.02720.04360.0715-0.21940.01520.1559-0.05640.03210.24230.01170.13340.8399-26.754912.2344
21.2204-0.50810.1651.2288-0.20431.16240.0076-0.18490.02860.122-0.0536-0.4664-0.09810.11120.04070.1311-0.0552-0.02030.17540.03170.318564.6691-17.11326.3653
32.2570.06420.19211.1025-0.20170.5737-0.01090.26930.0186-0.12060.0131-0.05060.1519-0.1343-0.00030.1473-0.05370.01940.23180.00510.108345.889-25.7558-2.5717
41.8740.3744-0.26542.0207-0.17540.96470.0066-0.0125-0.0196-0.17560.12130.0588-0.0165-0.407-0.07240.195-0.03620.01730.2520.02120.16843.7116-10.3589-1.8784
52.03981.7079-2.12281.797-1.85762.30480.03390.03850.31210.19670.05360.36240.0314-0.3334-0.02730.15260.02040.03970.217-0.03240.182342.3051-7.239511.758
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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