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

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Basic information

Entry
Database: PDB / ID: 1oxx
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
IODIDE ION / Glucose import ATP-binding protein GlcV
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.45 Å
AuthorsVerdon, G. / Albers, S.-V. / van Oosterwijk, N. / Dijkstra, B.W. / Driessen, A.J.M. / Thunnissen, A.M.W.H.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Formation of the productive ATP-Mg2+-bound dimer of GlcV, an ABC-ATPase from Sulfolobus solfataricus
Authors: Verdon, G. / Albers, S.-V. / van Oosterwijk, N. / Dijkstra, B.W. / Driessen, A.J.M. / Thunnissen, A.M.W.H.
History
DepositionApr 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)43,24233
Polymers39,1811
Non-polymers4,06132
Water12,502694
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.282, 48.427, 183.533
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: 39181.375 Da / Num. of mol.: 1 / Mutation: G144A
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.: 32 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 694 / 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: 2.11 Å3/Da / Density % sol: 41.25 %
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
Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: Verdon, G., (2002) Acta Crystallogr., D58, 362.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
14.25 mg/mlprotein1drop
215 %PEG33501reservoir
315 %PEG4001reservoir
40.1 MTris1reservoirpH8.3
50.5 M1reservoirNaCl
65 %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: Sep 5, 2001
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: 1.45→33.5 Å / Num. all: 62479 / Num. obs: 62479 / % possible obs: 80 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rsym value: 0.075 / Net I/σ(I): 14.3
Reflection shellResolution: 1.45→1.5 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.373 / % possible all: 31.2
Reflection
*PLUS
Redundancy: 2.93 % / Rmerge(I) obs: 0.075
Reflection shell
*PLUS
Lowest resolution: 1.5 Å / % possible obs: 31.2 % / Rmerge(I) obs: 0.373

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.45→33.52 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.953 / SU ML: 0.073 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.072 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21297 3100 5.1 %RANDOM
Rwork0.17239 ---
obs0.17449 57516 100 %-
all-57516 --
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: 10.859 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.45→33.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2707 0 32 694 3433
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222797
X-RAY DIFFRACTIONr_bond_other_d00.022725
X-RAY DIFFRACTIONr_angle_refined_deg1.371.9773780
X-RAY DIFFRACTIONr_angle_other_deg1.58736338
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4253351
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.23115550
X-RAY DIFFRACTIONr_chiral_restr0.1040.2446
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023048
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02535
X-RAY DIFFRACTIONr_nbd_refined0.2440.3590
X-RAY DIFFRACTIONr_nbd_other0.2230.32675
X-RAY DIFFRACTIONr_nbtor_other0.1120.52
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3250.5485
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2220.5
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.160.317
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2110.347
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5050.562
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it2.4811.51748
X-RAY DIFFRACTIONr_mcangle_it3.77722849
X-RAY DIFFRACTIONr_scbond_it6.09731049
X-RAY DIFFRACTIONr_scangle_it8.5844.5931
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.45→1.501 Å / Total num. of bins used: 15 /
RfactorNum. reflection
Rfree0.259 135
Rwork0.236 2372
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)
11.1716-0.2073-0.67510.34220.02350.7654-0.02010.0336-0.01880.0188-0.03180.0098-0.0767-0.0560.0520.0504-0.0087-0.00520.0713-0.03590.019911.66918.08617.734
2129.329181.6285-12.396721.69713.9701-4.87590.5348-5.2579-3.2170.364-4.7872-0.1241.6318-1.88384.25250.1675-0.22180.13830.4724-0.10260.391712.32310.96627.489
30.2648-0.04480.01761.01910.40190.1757-0.0027-0.0168-0.04730.0773-0.0096-0.0154-0.008-0.02310.01230.0417-0.0026-0.00550.061-0.00690.023517.6682.63411.917
40.75260.26460.19620.6226-0.06440.8291-0.0042-0.05740.01610.0238-0.02390.0297-0.0129-0.0070.02810.05870.0114-0.01150.0399-0.01240.021737.25822.50740.542
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1KA1 - 391 - 39
2X-RAY DIFFRACTION2KA40 - 4340 - 43
3X-RAY DIFFRACTION3KA44 - 22344 - 223
4X-RAY DIFFRACTION4KA224 - 352224 - 352
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 33.5 Å / Rfactor Rfree: 0.212 / Rfactor Rwork: 0.172
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.009
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.4
LS refinement shell
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 1.55 Å / Rfactor Rfree: 0.257 / Rfactor Rwork: 0.206

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