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- PDB-3sy4: Crystal structure of sulfide:quinone oxidoreductase Ser126Ala var... -

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Basic information

Entry
Database: PDB / ID: 3sy4
TitleCrystal structure of sulfide:quinone oxidoreductase Ser126Ala variant from Acidithiobacillus ferrooxidans
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 / 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 / FOURIER SYNTHESIS / Resolution: 1.91 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 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2012Group: Database references

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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
Water5,296294
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 operation9_555-x,-x+y,-z+1/31
Buried area6070 Å2
ΔGint-98 kcal/mol
Surface area34800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.766, 149.766, 81.730
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-613-

HOH

21A-737-

HOH

31A-752-

HOH

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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, 301 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.: 294 / 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: 2.77 Å3/Da / Density % sol: 55.61 %
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: 0.9795 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: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.91→81.6 Å / Num. obs: 38487 / % possible obs: 91.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 32.3 % / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 31.4
Reflection shellResolution: 1.91→2.01 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.992 / Mean I/σ(I) obs: 1.7 / Rsym value: 0.992 / % possible all: 64.7

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIXmodel building
PHENIX(phenix.refine: 1.7_650)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.91→69.147 Å / SU ML: 0.63 / σ(F): 1.37 / Phase error: 22.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2154 3753 5.18 %
Rwork0.1727 --
obs0.1748 38487 91.04 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.403 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.1515 Å20 Å20 Å2
2---4.1515 Å2-0 Å2
3---8.303 Å2
Refinement stepCycle: LAST / Resolution: 1.91→69.147 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3221 0 98 294 3613
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083405
X-RAY DIFFRACTIONf_angle_d1.1594617
X-RAY DIFFRACTIONf_dihedral_angle_d15.5061249
X-RAY DIFFRACTIONf_chiral_restr0.076500
X-RAY DIFFRACTIONf_plane_restr0.005584
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-1.93420.318700.36511508X-RAY DIFFRACTION53
1.9342-1.95970.3595750.31681674X-RAY DIFFRACTION59
1.9597-1.98650.35511180.28391825X-RAY DIFFRACTION66
1.9865-2.01490.35151180.27151999X-RAY DIFFRACTION72
2.0149-2.0450.24221160.25082134X-RAY DIFFRACTION76
2.045-2.07690.28861200.23742201X-RAY DIFFRACTION79
2.0769-2.1110.29031540.20942309X-RAY DIFFRACTION83
2.111-2.14740.26391260.20142372X-RAY DIFFRACTION85
2.1474-2.18640.27561380.21062568X-RAY DIFFRACTION91
2.1864-2.22850.29971280.18432635X-RAY DIFFRACTION94
2.2285-2.2740.23251580.18712790X-RAY DIFFRACTION99
2.274-2.32340.20811890.18412712X-RAY DIFFRACTION100
2.3234-2.37750.24361560.19022806X-RAY DIFFRACTION100
2.3775-2.43690.2331560.20142804X-RAY DIFFRACTION100
2.4369-2.50280.30571410.18692788X-RAY DIFFRACTION100
2.5028-2.57650.24471410.18982823X-RAY DIFFRACTION100
2.5765-2.65960.22121490.18112790X-RAY DIFFRACTION100
2.6596-2.75470.25061250.18862810X-RAY DIFFRACTION100
2.7547-2.8650.19511530.18862796X-RAY DIFFRACTION100
2.865-2.99540.24821500.18252813X-RAY DIFFRACTION100
2.9954-3.15330.24641810.17612762X-RAY DIFFRACTION100
3.1533-3.35090.17671560.18262781X-RAY DIFFRACTION100
3.3509-3.60960.20651560.17052786X-RAY DIFFRACTION100
3.6096-3.97280.19581340.14722820X-RAY DIFFRACTION100
3.9728-4.54760.16361380.12482827X-RAY DIFFRACTION100
4.5476-5.7290.18321410.132795X-RAY DIFFRACTION100
5.729-69.19220.17891660.17182792X-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)
11.89420.6402-0.24891.5057-0.32970.34160.0901-0.1888-0.11660.273-0.0666-0.0035-0.0041-0.1466-0.00590.2843-0.06320.02670.34970.04210.20740.5699-26.785512.2183
21.46020.2001-0.20411.7189-0.71830.88090.0863-0.1701-0.03530.1652-0.2334-0.7617-0.10970.14080.07540.2301-0.0551-0.05630.23810.06810.474164.4161-17.14296.1123
31.96170.65020.08081.5211-0.37490.4387-0.05250.2522-0.0428-0.17320.0509-0.15250.1246-0.1419-0.00830.243-0.04230.03410.31960.02040.213245.7479-25.8907-2.5476
41.49950.2519-0.45722.0129-0.49331.29020.16320.03050.203-0.01110.07320.1960.0361-0.3171-0.15770.1958-0.01780.02720.24570.04360.190543.6038-10.3178-1.9325
51.72281.2954-1.76921.2068-0.9351.6640.07930.11060.61080.4530.16920.3346-0.0347-0.2819-0.00810.36010.05970.10390.26480.03470.337341.9843-7.378411.496
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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