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- PDB-3t2z: Crystal structure of sulfide:quinone oxidoreductase from Acidithi... -

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Basic information

Entry
Database: PDB / ID: 3t2z
TitleCrystal structure of sulfide:quinone oxidoreductase from Acidithiobacillus ferrooxidans
ComponentsSulfide-quinone reductase, putative
KeywordsOXIDOREDUCTASE / sulfide:quinone oxidoreductase / integral monotopic membrane protein / acidithiobacillus ferrooxidans
Function / homology
Function and homology information


bacterial sulfide:quinone reductase / sulfide:quinone oxidoreductase activity / NAD(P)H dehydrogenase (quinone) activity / aerobic electron transport chain / 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
1,3-BUTANEDIOL / FLAVIN-ADENINE DINUCLEOTIDE / HYDROSULFURIC ACID / trisulfane / Sulfide-quinone reductase
Similarity search - Component
Biological speciesAcidithiobacillus ferrooxidans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2994 Å
AuthorsCherney, M.M. / Zhang, Y. / Solomonson, M. / Weiner, J.H. / James, M.N.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Crystal structure of sulfide:quinone oxidoreductase from Acidithiobacillus ferrooxidans: insights into sulfidotrophic respiration and detoxification.
Authors: Cherney, M.M. / Zhang, Y. / Solomonson, M. / Weiner, J.H. / James, M.N.
History
DepositionJul 23, 2011Deposition site: RCSB / Processing site: RCSB
SupersessionAug 17, 2011ID: 3KPI
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 13, 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_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_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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_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
B: Sulfide-quinone reductase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,87729
Polymers95,5322
Non-polymers3,34527
Water11,115617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9280 Å2
ΔGint-233 kcal/mol
Surface area30900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.729, 131.729, 208.864
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Sulfide-quinone reductase, putative


Mass: 47765.957 Da / Num. of mol.: 2
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, 644 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-BU2 / 1,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE


Mass: 34.081 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: H2S
#6: Chemical ChemComp-S3H / trisulfane


Mass: 98.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2S3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 617 / Source method: isolated from a natural source / Formula: H2O

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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: 4.74 Å3/Da / Density % sol: 74.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 30% PEG 600, 0.1 M bis-tris buffer, 0.1M (NH4)2SO4, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97945 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 3, 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: 2.299→50 Å / Num. all: 82166 / Num. obs: 82166 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 19.5
Reflection shellResolution: 2.299→2.38 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.986 / Mean I/σ(I) obs: 2 / Rsym value: 0.986 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3H27

3h27
PDB Unreleased entry


Resolution: 2.2994→40.918 Å / SU ML: 0.84 / σ(F): 1.34 / Phase error: 22.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2119 4105 5.01 %
Rwork0.1722 --
obs0.1742 82000 99.85 %
all-82116 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.847 Å2 / ksol: 0.341 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.2051 Å20 Å2-0 Å2
2--9.2051 Å20 Å2
3----18.4102 Å2
Refinement stepCycle: LAST / Resolution: 2.2994→40.918 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6544 0 189 617 7350
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076901
X-RAY DIFFRACTIONf_angle_d1.1899362
X-RAY DIFFRACTIONf_dihedral_angle_d16.2972574
X-RAY DIFFRACTIONf_chiral_restr0.072986
X-RAY DIFFRACTIONf_plane_restr0.0081186
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2994-2.32640.40591220.33942628X-RAY DIFFRACTION99
2.3264-2.35480.40631120.33742680X-RAY DIFFRACTION100
2.3548-2.38460.35191240.32512628X-RAY DIFFRACTION100
2.3846-2.4160.37481480.30542641X-RAY DIFFRACTION100
2.416-2.44910.35471550.29852621X-RAY DIFFRACTION100
2.4491-2.48410.3341430.27442650X-RAY DIFFRACTION100
2.4841-2.52110.27791230.2372668X-RAY DIFFRACTION100
2.5211-2.56050.25171240.2162658X-RAY DIFFRACTION100
2.5605-2.60250.24781400.20482664X-RAY DIFFRACTION100
2.6025-2.64740.23561470.20782654X-RAY DIFFRACTION100
2.6474-2.69550.27431610.21872626X-RAY DIFFRACTION100
2.6955-2.74730.27611310.21052684X-RAY DIFFRACTION100
2.7473-2.80340.28171410.20522673X-RAY DIFFRACTION100
2.8034-2.86430.24311640.18032627X-RAY DIFFRACTION100
2.8643-2.9310.22211370.17462671X-RAY DIFFRACTION100
2.931-3.00420.23441350.18312681X-RAY DIFFRACTION100
3.0042-3.08540.28371340.18282676X-RAY DIFFRACTION100
3.0854-3.17620.22311260.17992676X-RAY DIFFRACTION100
3.1762-3.27870.23561470.17872688X-RAY DIFFRACTION100
3.2787-3.39580.22361280.17512698X-RAY DIFFRACTION100
3.3958-3.53170.20481570.17432685X-RAY DIFFRACTION100
3.5317-3.69230.19421490.16422675X-RAY DIFFRACTION100
3.6923-3.88690.18471640.14812697X-RAY DIFFRACTION100
3.8869-4.13020.16611390.14452707X-RAY DIFFRACTION100
4.1302-4.44870.17021300.13372738X-RAY DIFFRACTION100
4.4487-4.89570.16051490.12072733X-RAY DIFFRACTION100
4.8957-5.60260.15861670.13072731X-RAY DIFFRACTION100
5.6026-7.05280.1791630.16382785X-RAY DIFFRACTION100
7.0528-40.9240.23041450.17562952X-RAY DIFFRACTION99

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