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

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Basic information

Entry
Database: PDB / ID: 1oxs
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 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Nucleic acid-binding, OB-fold / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / Glucose import ATP-binding protein GlcV
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / experimental phases derived from SAD data (iodide ions) / Resolution: 1.65 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. / J Driessen, A. / 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
C: ABC transporter, ATP binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,72129
Polymers39,1671
Non-polymers3,55328
Water8,323462
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.028, 48.267, 183.037
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.: 1
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: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 462 / 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: 2.24 Å3/Da / Density % sol: 44.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: PEG 3350, PEG 400, Tris, NaI, 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: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 10, 2000
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.65→45 Å / Num. all: 49451 / Num. obs: 49451 / % possible obs: 98.1 % / Observed criterion σ(F): 6 / Observed criterion σ(I): 6 / Redundancy: 5.8 % / Biso Wilson estimate: 19.562 Å2 / Rsym value: 0.068 / Net I/σ(I): 22.4
Reflection shellResolution: 1.65→1.69 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 5.9 / Num. unique all: 2966 / Rsym value: 0.373 / % possible all: 90.7
Reflection
*PLUS
Lowest resolution: 45 Å / Num. all: 49451 / Rmerge(I) obs: 0.068
Reflection shell
*PLUS
% possible obs: 90.7 % / Rmerge(I) obs: 0.373

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
SOLOMONphasing
ARP/wARPmodel building
RefinementMethod to determine structure: experimental phases derived from SAD data (iodide ions)
Resolution: 1.65→44.72 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.411 / SU ML: 0.084 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.089 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20857 3942 8 %RANDOM
Rwork0.1653 ---
obs0.16867 45286 99.54 %-
all-45286 --
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: 12.834 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.65→44.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2742 0 28 462 3232
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222803
X-RAY DIFFRACTIONr_bond_other_d0.0020.022714
X-RAY DIFFRACTIONr_angle_refined_deg1.6171.9793787
X-RAY DIFFRACTIONr_angle_other_deg1.48136320
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8833351
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.10215559
X-RAY DIFFRACTIONr_chiral_restr0.1190.2446
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023046
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02527
X-RAY DIFFRACTIONr_nbd_refined0.2450.3584
X-RAY DIFFRACTIONr_nbd_other0.2260.32703
X-RAY DIFFRACTIONr_nbtor_other0.210.54
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3250.5356
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4660.316
X-RAY DIFFRACTIONr_symmetry_vdw_other0.4240.339
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3510.540
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it3.5381.51748
X-RAY DIFFRACTIONr_mcangle_it8.49622851
X-RAY DIFFRACTIONr_scbond_it43.31531055
X-RAY DIFFRACTIONr_scangle_it40.2114.5936
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.708 Å / Total num. of bins used: 15 /
RfactorNum. reflection
Rfree0.241 356
Rwork0.172 4188
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)
11.5752-0.3597-0.60520.95810.3191.03380.0113-0.0198-0.0463-0.0482-0.07340.009-0.0743-0.02630.06210.1023-0.0031-0.01490.1026-0.03440.036711.31618.10817.747
227.4536-0.92223.347217.011-9.641326.38340.7418-1.7850.32961.0278-1.22640.15991.0548-1.6530.48460.306-0.10350.06270.3744-0.05580.016411.96311.33527.625
30.28290.025-0.05351.64710.70830.35060.0036-0.0358-0.06450.0925-0.0261-0.025-0.0155-0.04740.02250.1007-0.0019-0.00650.1151-0.00440.05717.2982.78712.087
41.30840.14410.24221.2928-0.311.4385-0.0113-0.05570.02920.0454-0.01760.0514-0.04210.00550.02890.08670.0005-0.01630.0703-0.01690.04436.85722.55240.417
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1CA1 - 391 - 39
2X-RAY DIFFRACTION2CA40 - 4340 - 43
3X-RAY DIFFRACTION3CA44 - 22344 - 223
4X-RAY DIFFRACTION4CA224 - 352224 - 352
Refinement
*PLUS
Lowest resolution: 45 Å / Rfactor Rfree: 0.209 / Rfactor Rwork: 0.165
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.016
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.62

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