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- PDB-3t2k: Crystal structure of sulfide:quinone oxidoreductase Cys128Ala var... -

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Basic information

Entry
Database: PDB / ID: 3t2k
TitleCrystal structure of sulfide:quinone oxidoreductase Cys128Ala variant from Acidithiobacillus ferrooxidans with bound trisulfane
ComponentsSulfide-quinone reductase, putative
KeywordsOXIDOREDUCTASE / sulfide:quinone oxidoreductase / Cys128Ala variant / integral monotopic membrane protein / complex with trisulfane
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 / trisulfane / Sulfide-quinone reductase
Similarity search - Component
Biological speciesAcidithiobacillus ferrooxidans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3501 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 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2012Group: Database references
Revision 1.2Jul 25, 2012Group: Other
Revision 1.3Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.4Nov 27, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / 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.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_label_atom_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2245
Polymers47,7341
Non-polymers1,4904
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)150.270, 150.270, 81.700
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: 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 , 4 types, 177 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-S3H / trisulfane


Mass: 98.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2S3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.79 Å3/Da / Density % sol: 55.9 %
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: 2.35→39 Å / Num. all: 23139 / Num. obs: 21404 / % possible obs: 92.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 40.659 Å2 / Rmerge(I) obs: 0.144 / Rsym value: 0.144 / Net I/σ(I): 6.5
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.789 / Mean I/σ(I) obs: 1.5 / Num. unique all: 3305 / Rsym value: 0.789 / % possible all: 100

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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: 2.3501→38.975 Å / SU ML: 0.76 / σ(F): 1.34 / Phase error: 26.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2638 2060 5.22 %random
Rwork0.1932 ---
obs0.1968 21404 91.82 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.764 Å2 / ksol: 0.333 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.6187 Å2-0 Å20 Å2
2---2.6187 Å2-0 Å2
3---5.2373 Å2
Refinement stepCycle: LAST / Resolution: 2.3501→38.975 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3221 0 96 174 3491
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073404
X-RAY DIFFRACTIONf_angle_d1.1584615
X-RAY DIFFRACTIONf_dihedral_angle_d15.5751243
X-RAY DIFFRACTIONf_chiral_restr0.073500
X-RAY DIFFRACTIONf_plane_restr0.007582
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3501-2.40480.36411590.3012699X-RAY DIFFRACTION100
2.4048-2.46490.31831500.3062704X-RAY DIFFRACTION100
2.4649-2.53150.36491810.31932633X-RAY DIFFRACTION98
2.5315-2.6060.36221410.2752712X-RAY DIFFRACTION100
2.606-2.69010.4386740.32691479X-RAY DIFFRACTION54
2.6901-2.78620.33941540.26862715X-RAY DIFFRACTION100
2.7862-2.89780.29771220.21692733X-RAY DIFFRACTION99
2.8978-3.02960.26751600.20582695X-RAY DIFFRACTION100
3.0296-3.18930.3021440.19442681X-RAY DIFFRACTION100
3.1893-3.3890.26731730.21162657X-RAY DIFFRACTION99
3.389-3.65050.30631130.18962019X-RAY DIFFRACTION78
3.6505-4.01750.2826820.15961678X-RAY DIFFRACTION74
4.0175-4.5980.20221190.12172702X-RAY DIFFRACTION99
4.598-5.790.16841550.13312661X-RAY DIFFRACTION98
5.79-38.98040.1971330.16782658X-RAY DIFFRACTION97
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)
11.57070.7507-0.18671.8422-0.38880.77290.0912-0.244-0.13260.3973-0.1238-0.04930.0064-0.1803-0.00660.2205-0.0944-0.00690.24610.03480.1340.7103-26.752412.296
21.00720.1755-0.30691.5406-0.23270.58310.1306-0.1597-0.12270.2975-0.2549-0.8267-0.12490.23340.02240.1664-0.0941-0.07060.19520.11430.497764.4952-16.98036.1709
32.37280.52580.23081.8331-0.44080.71710.03420.22360.0005-0.144-0.009-0.26470.1191-0.0736-0.03010.1577-0.04560.02380.220.02760.097945.9023-25.8588-2.5095
42.94610.7966-1.1792.8559-0.9520.8979-0.00290.06750.1306-0.17750.0750.107-0.1283-0.408-0.01480.18450.00580.04630.23370.02030.203943.5806-10.3177-2.0722
52.03691.8131-2.22441.6763-2.05693.0210.03310.08560.74460.35830.1180.49480.013-0.4597-0.12190.30490.04140.09720.2972-0.00360.315742.0738-7.388411.5074
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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