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

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Basic information

Entry
Database: PDB / ID: 3kpk
TitleCrystal structure of sulfide:quinone oxidoreductase from Acidithiobacillus ferrooxidans, C160A mutant
ComponentsSulfide-quinone reductase, putativeSulfide:quinone reductase
KeywordsOXIDOREDUCTASE / Oxidoreductases / Sulfide:quinone oxidoreductase / C160A mutant
Function / homology
Function and homology information


bacterial sulfide:quinone reductase / sulfide:quinone oxidoreductase 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 / R-1,2-PROPANEDIOL / Sulfide-quinone reductase
Similarity search - Component
Biological speciesAcidithiobacillus ferrooxidans ATCC 23270 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsCherney, M.M. / Zhang, Y. / Solomonson, M. / Weiner, J.H. / James, M.N.G.
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
DepositionNov 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sulfide-quinone reductase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8736
Polymers47,4331
Non-polymers1,4405
Water5,386299
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)150.080, 150.080, 81.679
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-570-

HOH

21A-592-

HOH

31A-680-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Sulfide-quinone reductase, putative / Sulfide:quinone reductase


Mass: 47432.574 Da / Num. of mol.: 1 / Mutation: C160A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidithiobacillus ferrooxidans ATCC 23270 (bacteria)
Strain: ATCC 23270 / DSM 14882 / NCIB 8455 / Gene: AFE_1792 / Plasmid: PLM1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / 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, 303 molecules

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


Mass: 34.081 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2S
#5: Chemical ChemComp-PGR / R-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 2.8 Å3/Da / Density % sol: 56.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 30% PEG 600, 0.1 M bis-tris buffer, 0.1M MgSO4, 0.4mM DDM, 5% ethylene glycole, 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: 0.97946 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 33814 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 39.1 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 31.7
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.814 / Mean I/σ(I) obs: 1.55 / Num. unique all: 3367 / Rsym value: 0.814 / % possible all: 85.5

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.4_4)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3kpg

3kpg
PDB Unreleased entry


Resolution: 2.05→34.578 Å / SU ML: 0.35 / σ(F): 1.35
RfactorNum. reflection% reflection
Rfree0.2312 1708 5.05 %
Rwork0.1845 --
obs0.1868 33789 98.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.798 Å2 / ksol: 0.334 e/Å3
Refinement stepCycle: LAST / Resolution: 2.05→34.578 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3200 0 95 299 3594
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073381
X-RAY DIFFRACTIONf_angle_d1.1834583
X-RAY DIFFRACTIONf_dihedral_angle_d20.2181258
X-RAY DIFFRACTIONf_chiral_restr0.083498
X-RAY DIFFRACTIONf_plane_restr0.005578
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.11080.32151330.28182249X-RAY DIFFRACTION84
2.1108-2.17890.29011500.25632485X-RAY DIFFRACTION94
2.1789-2.25680.28611380.23312662X-RAY DIFFRACTION100
2.2568-2.34710.26971410.2092702X-RAY DIFFRACTION100
2.3471-2.45390.25991440.1982675X-RAY DIFFRACTION100
2.4539-2.58330.2851320.19782708X-RAY DIFFRACTION100
2.5833-2.7450.27531460.2032690X-RAY DIFFRACTION100
2.745-2.95690.26291690.19582698X-RAY DIFFRACTION100
2.9569-3.25420.23691280.18852741X-RAY DIFFRACTION100
3.2542-3.72470.22251370.16762753X-RAY DIFFRACTION100
3.7247-4.69080.16951470.14312765X-RAY DIFFRACTION100
4.6908-34.58330.19381430.16662953X-RAY DIFFRACTION100
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined1.09781.0506-0.19343.664-0.650.54390.1127-0.0684-0.07360.2491-0.1565-0.34040.0228-0.16680.04240.1503-0.0578-0.01230.26980.04110.128933.835-2.79057.6674
20.2074-0.05740.05490.1806-0.12820.08820.40670.1160.6378-0.08480.0106-0.0675-0.2172-0.1531-0.36141.0681-0.11080.34140.93850.05171.1496
Refinement TLS groupSelection details: chain A and resid 407:418

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