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- PDB-3hyx: 3-D X-Ray structure of the sulfide:quinone oxidoreductase from Aq... -

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Basic information

Entry
Database: PDB / ID: 3hyx
Title3-D X-Ray structure of the sulfide:quinone oxidoreductase from Aquifex aeolicus in complex with Aurachin C
ComponentsSulfide-quinone reductase
KeywordsOXIDOREDUCTASE / MONOTOPIC MEMBRANE PROTEIN / SULFIDE OXIDATION / ROSSMANN-FOLD DOMAIN / FLAVOPROTEIN / QUINONE REDUCTION
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 / identical protein 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-AUK / FLAVIN-ADENINE DINUCLEOTIDE / HYDROSULFURIC ACID / octathiocane / Sulfide-quinone reductase
Similarity search - Component
Biological speciesAQUIFEX AEOLICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsMarcia, M. / Ermler, U. / Peng, G.H. / Michel, H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: The structure of Aquifex aeolicus sulfide:quinone oxidoreductase, a basis to understand sulfide detoxification and respiration
Authors: Marcia, M. / Ermler, U. / Peng, G.H. / Michel, H.
History
DepositionJun 23, 2009Deposition site: RCSB / Processing site: PDBJ
SupersessionJul 14, 2009ID: 3H29
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / 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_asym_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_asym_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.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sulfide-quinone reductase
B: Sulfide-quinone reductase
C: Sulfide-quinone reductase
D: Sulfide-quinone reductase
E: Sulfide-quinone reductase
F: Sulfide-quinone reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)299,31360
Polymers285,2106
Non-polymers14,10354
Water3,495194
1
A: Sulfide-quinone reductase
C: Sulfide-quinone reductase
E: Sulfide-quinone reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,65630
Polymers142,6053
Non-polymers7,05227
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sulfide-quinone reductase
D: Sulfide-quinone reductase
F: Sulfide-quinone reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,65630
Polymers142,6053
Non-polymers7,05227
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Sulfide-quinone reductase
D: Sulfide-quinone reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,86721
Polymers95,0702
Non-polymers4,79719
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8620 Å2
ΔGint-154 kcal/mol
Surface area31880 Å2
MethodPISA
4
A: Sulfide-quinone reductase
B: Sulfide-quinone reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,77120
Polymers95,0702
Non-polymers4,70118
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8340 Å2
ΔGint-155 kcal/mol
Surface area31630 Å2
MethodPISA
5
E: Sulfide-quinone reductase
F: Sulfide-quinone reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,67519
Polymers95,0702
Non-polymers4,60517
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8490 Å2
ΔGint-156 kcal/mol
Surface area31650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.180, 154.230, 176.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 12 molecules ABCDEF

#1: Protein
Sulfide-quinone reductase / sulfide:quinone oxidoreductase


Mass: 47534.918 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) AQUIFEX AEOLICUS (bacteria) / Strain: VF5
References: UniProt: O67931, Oxidoreductases; Acting on a sulfur group of donors; With a quinone or similar compound as acceptor
#5: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 6 types, 242 molecules

#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical
ChemComp-AUK / 1-hydroxy-2-methyl-3-[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trien-1-yl]quinolin-4(1H)-one / Aurachin C


Mass: 379.535 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C25H33NO2
#6: Chemical
ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE


Mass: 34.081 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: H2S
#7: Chemical
ChemComp-PS9 / octathiocane


Mass: 256.520 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: S8
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsTHE SIDE CHAIN OF CYS156 IS EXTENDED TO FORM A PUTATIVE POLYSULFUR CHAIN. ONE SULFUR ATOM OF THE ...THE SIDE CHAIN OF CYS156 IS EXTENDED TO FORM A PUTATIVE POLYSULFUR CHAIN. ONE SULFUR ATOM OF THE CHAIN IS DESCRIBED AS LINKED TO THE CYS AND FORM A S-MERCAPTO-CYSTEINE, CSS. THE REST OF THE CHAIN TAKES THE FORM OF A CYCLOOCTASULFUR SPECIES PS9 IN SEVERAL MONOMERS AND MIGHT REPRESENT THE PRODUCT OF THE REACTION CATALYZED BY THE PROTEIN. H2S INDICATES A PUTATIVE S ATOM BRIDGING CYS124 AND FAD. THIS S ATOM IS POSSIBLY CONTRIBUTED BY THE SUBSTRATE OF THE PROTEIN, HYDROGEN SULFIDE. PLEASE REFER TO THE RELATED PUBLICATION FOR A MORE DETAILED DESCRIPTION OF THE PUTATIVE SULFUR LIGANDS OF THE SULFIDE:QUINONE OXIDOREDUCTASE.

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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: 2.65 Å3/Da / Density % sol: 53.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 4% PEG 400, 2M AMMONIUM SULFATE, 0.1M NA-ACETATE, PH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00148 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 27, 2008 / Details: DYNAMICALLY BENDABLE MIRROR
RadiationMonochromator: LN2 COOLED FIXED-EXIT SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00148 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 67131 / % possible obs: 98.8 % / Redundancy: 3.72 % / Net I/σ(I): 16.74
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.41 % / Mean I/σ(I) obs: 4.05 / % possible all: 95.7

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Processing

Software
NameVersionClassification
XDSdata scaling
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
REFMAC5.2.0019phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3H27

3h27
PDB Unreleased entry


Resolution: 2.9→20.13 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.892 / SU B: 33.278 / SU ML: 0.314 / Cross valid method: THROUGHOUT / ESU R Free: 0.41 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23996 3388 5.1 %RANDOM
Rwork0.18054 ---
obs0.18358 63561 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.734 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å20 Å2
2---0.16 Å20 Å2
3---0.51 Å2
Refinement stepCycle: LAST / Resolution: 2.9→20.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20016 0 869 194 21079
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02221573
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2552.01129326
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.35552590
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.85624.407869
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.64153412
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1391584
X-RAY DIFFRACTIONr_chiral_restr0.0780.23173
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0216126
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.210056
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.214500
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2795
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3581.513218
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.615220976
X-RAY DIFFRACTIONr_scbond_it0.895310050
X-RAY DIFFRACTIONr_scangle_it1.5174.58339
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.974 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 246 -
Rwork0.282 4356 -
obs--94.38 %

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