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- PDB-1oxt: Crystal structure of GlcV, the ABC-ATPase of the glucose ABC tran... -

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Basic information

Entry
Database: PDB / ID: 1oxt
TitleCrystal structure of GlcV, the ABC-ATPase of the glucose ABC transporter from Sulfolobus solfataricus
ComponentsABC transporter, ATP binding protein
KeywordsTRANSPORT PROTEIN / ABC-ATPase / ATP-binding cassette / ATPase / GlcV / Sulfolobus solfataricus
Function / homology
Function and homology information


ABC-type ferric iron transporter activity / Translocases; Catalysing the translocation of carbohydrates and their derivatives; Linked to the hydrolysis of a nucleoside triphosphate / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP hydrolysis activity / ATP binding
Similarity search - Function
Glucose ABC transporter, C-terminal / : / Glucose ABC transporter C-terminal domain / ABC transporter, ferric cation import, FbpC / : / Molybdate/tungstate binding, C-terminal / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Nucleic acid-binding proteins / ABC transporter-like, conserved site / ABC transporters family signature. ...Glucose ABC transporter, C-terminal / : / Glucose ABC transporter C-terminal domain / ABC transporter, ferric cation import, FbpC / : / Molybdate/tungstate binding, C-terminal / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Nucleic acid-binding proteins / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / P-loop containing nucleotide triphosphate hydrolases / Nucleic acid-binding, OB-fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Glucose import ATP-binding protein GlcV
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsVerdon, G. / Albers, S.V. / Dijkstra, B.W. / Driessen, A.J. / Thunnissen, A.M.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: Crystal structures of the ATPase subunit of the glucose ABC transporter from Sulfolobus solfataricus: nucleotide-free and nucleotide-bound conformations
Authors: Verdon, G. / Albers, S.V. / Dijkstra, B.W. / Driessen, A.J. / Thunnissen, A.M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Purification, crystallization and preliminary X-ray diffraction analysis of an archaeal ABC-ATPase
Authors: Verdon, G. / Albers, S.V. / Dijkstra, B.W. / Driessen, A.J. / Thunnissen, A.M.
#2: Journal: J.Bacteriol. / Year: 1999
Title: Glucose transport in the extremely thermoacidophilic Sulfolobus solfataricus involves a high-affinity membrane-integrated binding protein
Authors: Albers, S.V. / Elferink, M.G. / Charlebois, R.L. / Sensen, C.W. / Driessen, A.J. / Konings, W.N.
History
DepositionApr 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ABC transporter, ATP binding protein
B: ABC transporter, ATP binding protein
D: ABC transporter, ATP binding protein


Theoretical massNumber of molelcules
Total (without water)117,5023
Polymers117,5023
Non-polymers00
Water11,548641
1
A: ABC transporter, ATP binding protein


Theoretical massNumber of molelcules
Total (without water)39,1671
Polymers39,1671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ABC transporter, ATP binding protein


Theoretical massNumber of molelcules
Total (without water)39,1671
Polymers39,1671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: ABC transporter, ATP binding protein


Theoretical massNumber of molelcules
Total (without water)39,1671
Polymers39,1671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.032, 146.641, 178.493
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ABC transporter, ATP binding protein / GlcV / glucose


Mass: 39167.348 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: glcV / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: Q97UY8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 641 / 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: 2.52 Å3/Da / Density % sol: 50.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: PEG 3350, PEG 400, Tris, NaCl, glycerol, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
14.25 mg/mlprotein1drop
220 mMMES1droppH6.5
3150 mM1dropNaCl
45 %(v/v)glycerol1drop
55 mM1dropMgCl2
615 %(w/v)PEG33501reservoir
715 %(w/v)PEG4001reservoir
80.1 MTris1reservoirpH8.3
90.5 M1reservoirNaI
1015 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationMonochromator: Double crystal, Si(111) or Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→45 Å / Num. all: 69924 / Num. obs: 69924 / % possible obs: 95.4 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Rsym value: 0.057 / Net I/σ(I): 20.5
Reflection shellResolution: 2.1→2.2 Å / Mean I/σ(I) obs: 3 / Rsym value: 0.336 / % possible all: 71
Reflection
*PLUS
Highest resolution: 2.1 Å / Num. all: 69924 / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
Highest resolution: 2.1 Å / % possible obs: 71 % / Rmerge(I) obs: 0.336

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→45.64 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.914 / SU B: 5.522 / SU ML: 0.147 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.242 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27467 3570 5.1 %RANDOM
Rwork0.21435 ---
obs0.21742 66288 100 %-
all-66288 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.107 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2---0.09 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.1→45.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8025 0 0 641 8666
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0228190
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1221.97611072
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.2531053
X-RAY DIFFRACTIONr_dihedral_angle_2_deg17.375151555
X-RAY DIFFRACTIONr_chiral_restr0.0750.21291
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026040
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2670.33875
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.5882
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3920.385
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined1.1060.549
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it5.3641.55216
X-RAY DIFFRACTIONr_mcangle_it6.88728422
X-RAY DIFFRACTIONr_scbond_it11.1732974
X-RAY DIFFRACTIONr_scangle_it14.1654.52650
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.174 Å / Total num. of bins used: 15 /
RfactorNum. reflection
Rfree0.311 262
Rwork0.242 4934
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)
12.39470.0630.00141.2549-0.19782.8465-0.053-0.07850.1045-0.0583-0.0164-0.02730.10220.19070.06930.13030.03830.01890.05760.04780.073715.8249.08114.509
22.4339-0.1152-0.70012.95530.15452.4686-0.0529-0.09360.02010.1424-0.0324-0.06490.02070.05990.08530.0569-0.0048-0.02260.0040.01630.06636.6633.1747.333
30.9840.1496-0.68843.439-2.6432.2583-0.0411-0.25160.18040.40350.06990.1803-0.2586-0.0829-0.02890.18680.0020.03030.1074-0.00210.10410.69114.65418.578
45.9498-0.1801-2.4181.86410.02093.5143-0.2241-0.7054-0.440.16730.07980.02340.31280.20080.14440.21940.02570.03620.15460.1130.1391-12.876-0.58939.766
52.18980.0769-0.00570.7872-0.15372.6488-0.0651-0.04490.1745-0.0093-0.0185-0.03930.04140.10540.08360.14330.01720.0030.03970.01450.055915.84757.01214.412
62.6061-0.2557-1.51043.6962-0.53983.00520.09930.1180.39970.1299-0.0413-0.0657-0.13030.0859-0.0580.17-0.0061-0.00450.08080.0460.25046.58281.5056.523
71.71690.1201-0.91913.0336-2.34292.8317-0.0248-0.1310.30120.42940.06450.1824-0.3525-0.1377-0.03960.19450.00570.01980.0968-0.00880.09380.73562.68218.431
86.7952-0.5436-2.79071.97960.61283.5114-0.2679-0.7954-0.45410.16790.09460.12070.39670.16420.17330.22830.00780.04810.17260.0740.1072-12.75348.08239.844
92.5616-0.2753-0.14532.0935-0.20633.81040.1624-0.0993-0.20430.064-0.20120.10480.32420.40640.03880.4013-0.01340.050.2010.00420.256814.482106.65612.58
102.7904-0.0379-0.78883.26460.62122.8366-0.15510.16580.06630.08090.03840.01380.1242-0.0040.11670.1729-0.0253-0.0370.07680.03990.17086.498132.1986.476
112.87930.4662-1.25795.242-3.38072.4827-0.0888-0.1689-0.08380.66540.01850.5571-0.17070.01670.07030.4594-0.06760.16260.1886-0.08870.3089-0.23113.14417.422
123.37841.0402-2.8643.3746-1.32694.5254-0.2377-0.179-0.2801-0.07650.0749-0.21530.4138-0.09790.16280.3997-0.08360.08750.22790.00320.3569-14.05997.01737.504
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 881 - 88
2X-RAY DIFFRACTION2AA89 - 16089 - 160
3X-RAY DIFFRACTION3AA161 - 225161 - 225
4X-RAY DIFFRACTION4AA226 - 352226 - 352
5X-RAY DIFFRACTION5BB1 - 881 - 88
6X-RAY DIFFRACTION6BB93 - 16093 - 160
7X-RAY DIFFRACTION7BB161 - 225161 - 225
8X-RAY DIFFRACTION8BB226 - 352226 - 352
9X-RAY DIFFRACTION9DC1 - 881 - 88
10X-RAY DIFFRACTION10DC93 - 16093 - 160
11X-RAY DIFFRACTION11DC161 - 225161 - 225
12X-RAY DIFFRACTION12DC226 - 352226 - 352
Refinement
*PLUS
Lowest resolution: 45 Å / Rfactor Rfree: 0.275 / Rfactor Rwork: 0.215
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.01
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.12

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