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- PDB-3t14: Crystal structure of sulfide:quinone oxidoreductase Cys128Ala var... -

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Basic information

Entry
Database: PDB / ID: 3t14
TitleCrystal structure of sulfide:quinone oxidoreductase Cys128Ala variant from Acidithiobacillus ferrooxidans with bound disulfide
ComponentsSulfide-quinone reductase, putativeSulfide:quinone reductase
KeywordsOXIDOREDUCTASE / sulfide:quinone oxidoreductase / Cys128Ala variant / integral monotopic membrane protein / complex with disulfide
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 / Hydrogen disulfide / Sulfide-quinone reductase
Similarity search - Component
Biological speciesAcidithiobacillus ferrooxidans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.21 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 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2012Group: Database references
Revision 1.2May 7, 2014Group: Other
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name

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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)49,4188
Polymers47,7341
Non-polymers1,6857
Water3,333185
1
A: Sulfide-quinone reductase, putative
hetero molecules

A: Sulfide-quinone reductase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,83716
Polymers95,4682
Non-polymers3,36914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area1740 Å2
ΔGint-10 kcal/mol
Surface area34380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.700, 149.700, 81.400
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 / Sulfide:quinone reductase


Mass: 47733.895 Da / Num. of mol.: 1 / Mutation: C128A
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 , 5 types, 191 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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE / Hydrogen sulfide


Mass: 34.081 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2S
#6: Chemical ChemComp-S2H / Hydrogen disulfide / Hydrogen disulfide


Mass: 66.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2S2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.76 Å3/Da / Density % sol: 55.4 %
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: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 28, 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: 2.21→43.22 Å / Num. all: 27334 / Num. obs: 24355 / % possible obs: 89.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.8 % / Biso Wilson estimate: 40.4 Å2 / Rmerge(I) obs: 0.142 / Rsym value: 0.142 / Net I/σ(I): 9.5
Reflection shellResolution: 2.21→2.33 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.978 / Mean I/σ(I) obs: 2 / Num. unique all: 3889 / Rsym value: 0.978 / % possible all: 69.5

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIX(phenix.refine: 1.7.1_743)model building
PHENIX(phenix.refine: 1.7.1_743)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIX1.7.1_743phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.21→43.215 Å / SU ML: 0.76 / σ(F): 1.34 / Phase error: 24.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2329 2331 5.12 %random
Rwork0.1733 ---
obs0.1763 24355 89.01 %-
all-51111 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.731 Å2 / ksol: 0.337 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.7539 Å20 Å20 Å2
2---3.7539 Å2-0 Å2
3---7.5079 Å2
Refinement stepCycle: LAST / Resolution: 2.21→43.215 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3221 0 106 185 3512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083416
X-RAY DIFFRACTIONf_angle_d1.1274632
X-RAY DIFFRACTIONf_dihedral_angle_d21.1161284
X-RAY DIFFRACTIONf_chiral_restr0.071501
X-RAY DIFFRACTIONf_plane_restr0.007583
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.21-2.25510.4268720.31531313X-RAY DIFFRACTION82
2.2551-2.30410.29191170.27052243X-RAY DIFFRACTION99
2.3041-2.35770.28121610.24162781X-RAY DIFFRACTION99
2.3577-2.41670.29091200.25212844X-RAY DIFFRACTION99
2.4167-2.4820.33771620.23672824X-RAY DIFFRACTION99
2.482-2.55510.28021580.21372819X-RAY DIFFRACTION99
2.5551-2.63750.25831680.21382821X-RAY DIFFRACTION99
2.6375-2.73180.3396880.22361595X-RAY DIFFRACTION56
2.7318-2.84110.35751660.21862812X-RAY DIFFRACTION99
2.8411-2.97040.29071470.19732818X-RAY DIFFRACTION100
2.9704-3.1270.28151620.18042859X-RAY DIFFRACTION99
3.127-3.32280.22021840.18062798X-RAY DIFFRACTION100
3.3228-3.57930.22821110.15922318X-RAY DIFFRACTION81
3.5793-3.93920.1469950.14341718X-RAY DIFFRACTION74
3.9392-4.50870.17321400.12482866X-RAY DIFFRACTION100
4.5087-5.67850.17851500.12392854X-RAY DIFFRACTION100
5.6785-43.22290.221300.17122875X-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)
13.46490.8098-0.14721.9931-0.32520.8730.026-0.3565-0.11950.3762-0.03910.14030.004-0.2625-0.00150.2838-0.0430.04270.32290.03280.216740.626-26.79612.2489
22.2266-0.4853-0.16112.9572-0.51951.99260.0682-0.19410.04410.2866-0.1128-0.76-0.16590.30710.04580.2098-0.0626-0.04250.25680.03380.463564.4148-17.14796.1879
34.25120.4461-0.10061.9383-0.50870.8876-0.00810.3380.057-0.12670.0687-0.07450.1488-0.2185-0.05210.2177-0.03820.00810.2728-0.00020.173145.7678-25.8313-2.5634
42.43550.9182-0.37883.7845-0.13212.31250.06040.01720.2125-0.2220.10260.32930.0054-0.5914-0.11920.2041-0.00570.04540.27480.04440.303243.6347-10.3095-1.882
54.05073.3772-3.79083.4281-2.84323.57990.14420.05920.89740.44340.12860.68310.0521-0.4303-0.25190.37180.06280.10650.3501-0.0220.420742.1025-7.343311.6873
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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