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- PDB-3syi: Crystal structure of sulfide:quinone oxidoreductase Ser126Ala var... -

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Basic information

Entry
Database: PDB / ID: 3syi
TitleCrystal structure of sulfide:quinone oxidoreductase Ser126Ala variant from Acidithiobacillus ferrooxidans using 7.0 keV diffraction data
ComponentsSulfide-quinone reductase, putative
KeywordsOXIDOREDUCTASE / sulfide:quinone oxidoreductase / Ser126Ala variant / integral monotopic membrane protein / complex with sulfide
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
FLAVIN-ADENINE DINUCLEOTIDE / HYDROSULFURIC ACID / Sulfide-quinone reductase
Similarity search - Component
Biological speciesAcidithiobacillus ferrooxidans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / refinement / Resolution: 2.2001 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 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2012Group: Database references
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_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

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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)49,3139
Polymers47,7501
Non-polymers1,5638
Water1,874104
1
A: Sulfide-quinone reductase, putative
hetero molecules

A: Sulfide-quinone reductase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,62518
Polymers95,5002
Non-polymers3,12516
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/31
Buried area6690 Å2
ΔGint-102 kcal/mol
Surface area34560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.790, 149.790, 81.911
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 / Sugars , 2 types, 2 molecules A

#1: Protein Sulfide-quinone reductase, putative


Mass: 47749.957 Da / Num. of mol.: 1 / Mutation: S126A
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 , 4 types, 111 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-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE


Mass: 34.081 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: H2S
#5: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.78 Å3/Da / Density % sol: 55.72 %
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: 1.7712 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 12, 2010
RadiationMonochromator: ACCEL/BRUKER double crystal monochromator (DCM), featuring indirectly cryo-cooled first crystal and sagittally focusing second crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7712 Å / Relative weight: 1
ReflectionResolution: 2.2→49 Å / Num. obs: 48437 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.2 % / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Net I/σ(I): 14.5
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.833 / Mean I/σ(I) obs: 1.3 / Rsym value: 0.833 / % possible all: 69.2

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIXmodel building
PHENIX(phenix.refine: 1.7.1_743)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: refinement
Starting model: PDB ENTRY 3KPG

3kpg
PDB Unreleased entry


Resolution: 2.2001→42.069 Å / SU ML: 0.7 / σ(F): 1.34 / Phase error: 27.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2382 2435 5.03 %
Rwork0.1871 --
obs0.1897 48437 92.78 %
all-52196 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.876 Å2 / ksol: 0.332 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.5118 Å2-0 Å20 Å2
2---5.5118 Å2-0 Å2
3---11.0236 Å2
Refinement stepCycle: LAST / Resolution: 2.2001→42.069 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3221 0 98 104 3423
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093399
X-RAY DIFFRACTIONf_angle_d1.194608
X-RAY DIFFRACTIONf_dihedral_angle_d21.0381280
X-RAY DIFFRACTIONf_chiral_restr0.073499
X-RAY DIFFRACTIONf_plane_restr0.009582
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.2450.3957670.42071166X-RAY DIFFRACTION40
2.245-2.29380.3934940.39631872X-RAY DIFFRACTION64
2.2938-2.34720.32451070.31462473X-RAY DIFFRACTION84
2.3472-2.40580.30781510.30842662X-RAY DIFFRACTION92
2.4058-2.47090.34771340.26832869X-RAY DIFFRACTION98
2.4709-2.54360.30931390.24622926X-RAY DIFFRACTION100
2.5436-2.62570.3291520.2592926X-RAY DIFFRACTION100
2.6257-2.71950.25271480.24942912X-RAY DIFFRACTION100
2.7195-2.82840.33991610.2422907X-RAY DIFFRACTION100
2.8284-2.95710.26081660.22292905X-RAY DIFFRACTION100
2.9571-3.11290.32271600.22412898X-RAY DIFFRACTION100
3.1129-3.30790.28621810.20812897X-RAY DIFFRACTION100
3.3079-3.56320.24881850.1822903X-RAY DIFFRACTION100
3.5632-3.92150.23411390.1662918X-RAY DIFFRACTION100
3.9215-4.48840.16231800.13062891X-RAY DIFFRACTION100
4.4884-5.65270.17731450.12062926X-RAY DIFFRACTION100
5.6527-42.0770.18041260.16352951X-RAY DIFFRACTION100

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