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- PDB-3szw: Crystal structure of sulfide:quinone oxidoreductase Cys128Ser var... -

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Basic information

Entry
Database: PDB / ID: 3szw
TitleCrystal structure of sulfide:quinone oxidoreductase Cys128Ser variant from Acidithiobacillus ferrooxidans in complex with decylubiquinone
ComponentsSulfide-quinone reductase, putative
KeywordsOXIDOREDUCTASE / sulfide:quinone oxidoreductase / Cys128Ser variant / integral monotopic membrane protein / complex with decylubiquinone
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
Chem-DCQ / FLAVIN-ADENINE DINUCLEOTIDE / HYDROSULFURIC ACID / Sulfide-quinone reductase
Similarity search - Component
Biological speciesAcidithiobacillus ferrooxidans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / refinement / Resolution: 2.2 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 19, 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 1.3Sep 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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)49,6019
Polymers47,7501
Non-polymers1,8518
Water5,170287
1
A: Sulfide-quinone reductase, putative
hetero molecules

A: Sulfide-quinone reductase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,20218
Polymers95,5002
Non-polymers3,70216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area1820 Å2
ΔGint-11 kcal/mol
Surface area34140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.907, 149.907, 81.386
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: 47749.895 Da / Num. of mol.: 1 / Mutation: C128S
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, 294 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-DCQ / 2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione / decylubiquinone


Mass: 322.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H30O4
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE


Mass: 34.081 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H2S
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 55.5 %
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, 5 mM decylubiquinone, 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: 0.97945 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 10, 2010
RadiationMonochromator: ACCEL/BRUKER double crystal monochromator (DCM)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.2→75 Å / Num. all: 27876 / Num. obs: 27876 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 21.5 % / Rsym value: 0.16 / Net I/σ(I): 19
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 21.6 % / Rmerge(I) obs: 1.113 / Mean I/σ(I) obs: 3.1 / Rsym value: 1.113 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX(phenix.refine: 1.7_650)model building
PHENIX(phenix.refine: 1.7_650)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIX1.7_650phasing
RefinementMethod to determine structure: refinement
Starting model: PDB ENTRY 3T31

3t31


Resolution: 2.2→50.748 Å / SU ML: 0.68 / σ(F): 1.35 / Phase error: 21.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.219 1344 5.04 %
Rwork0.1678 --
obs0.1704 27876 99.99 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.88 Å2 / ksol: 0.341 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.5451 Å2-0 Å20 Å2
2---4.5451 Å2-0 Å2
3---9.0903 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3222 0 120 287 3629
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073438
X-RAY DIFFRACTIONf_angle_d1.1094661
X-RAY DIFFRACTIONf_dihedral_angle_d16.4011291
X-RAY DIFFRACTIONf_chiral_restr0.069495
X-RAY DIFFRACTIONf_plane_restr0.008587
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.240.36961490.28322604X-RAY DIFFRACTION100
2.24-2.28310.28451110.26282607X-RAY DIFFRACTION100
2.2831-2.32970.28481350.21412619X-RAY DIFFRACTION100
2.3297-2.38040.26551320.22592581X-RAY DIFFRACTION100
2.3804-2.43570.23971380.20582610X-RAY DIFFRACTION100
2.4357-2.49670.26941400.20622575X-RAY DIFFRACTION100
2.4967-2.56420.24991100.19992627X-RAY DIFFRACTION100
2.5642-2.63960.29451390.19312593X-RAY DIFFRACTION100
2.6396-2.72480.23081490.18512586X-RAY DIFFRACTION100
2.7248-2.82220.21141470.17432595X-RAY DIFFRACTION100
2.8222-2.93520.24941470.17312577X-RAY DIFFRACTION100
2.9352-3.06870.2521480.1742594X-RAY DIFFRACTION100
3.0687-3.23050.21911340.17242589X-RAY DIFFRACTION100
3.2305-3.43290.21491370.16042584X-RAY DIFFRACTION100
3.4329-3.69780.2151530.16192617X-RAY DIFFRACTION100
3.6978-4.06980.20441780.14252546X-RAY DIFFRACTION100
4.0698-4.65840.16641140.11072620X-RAY DIFFRACTION100
4.6584-5.86770.15441470.12842600X-RAY DIFFRACTION100
5.8677-50.7610.1911110.17442628X-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)
11.99620.2988-0.25521.1056-0.24670.59780.006-0.1567-0.16860.21180.01110.09760.0669-0.2284-0.01390.1873-0.04840.02580.25210.05060.174140.6246-26.717112.2596
21.6594-0.2358-0.11851.9287-0.47451.76050.1035-0.1839-0.00090.1592-0.0614-0.5293-0.12830.1834-0.01350.161-0.043-0.03460.17230.03290.337464.503-17.21266.259
32.62390.4035-0.05921.4738-0.35580.81610.01570.2792-0.1076-0.1190.0425-0.04530.1839-0.1587-0.04480.1715-0.04020.01090.20280.01890.111645.7029-25.7392-2.4892
41.53350.49520.10492.5562-0.08871.4538-0.0155-0.02820.0874-0.14720.13010.1470.0398-0.3849-0.07490.1792-0.01530.05080.23250.03650.187543.7074-10.2752-1.8365
52.26381.6207-2.27952.0573-1.63352.45980.06920.05470.3950.39780.15850.3597-0.0265-0.3731-0.18750.27070.04160.06380.27950.02980.262542.1242-7.209211.6666
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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