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

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Basic information

Entry
Database: PDB / ID: 1oxu
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
ADENOSINE-5'-DIPHOSPHATE / IODIDE ION / : / 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: ABC transporter, ATP binding protein
B: ABC transporter, ATP binding protein
C: ABC transporter, ATP binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,47169
Polymers117,5023
Non-polymers8,96966
Water14,592810
1
A: ABC transporter, ATP binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,66527
Polymers39,1671
Non-polymers3,49726
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ABC transporter, ATP binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,52218
Polymers39,1671
Non-polymers2,35517
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: ABC transporter, ATP binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,28424
Polymers39,1671
Non-polymers3,11623
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.402, 149.045, 176.422
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: GenBank: 15899565, UniProt: Q97UY8*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 60 / Source method: obtained synthetically / Formula: I
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 810 / 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: 2.45 Å3/Da / Density % sol: 49.45 %
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: BM30A / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 28, 2000
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.1→35 Å / Num. all: 73299 / Num. obs: 73299 / % possible obs: 98.9 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 4 / Rsym value: 0.079 / Net I/σ(I): 16.2
Reflection shellResolution: 2.1→2.15 Å / Mean I/σ(I) obs: 3.9 / Rsym value: 0.342 / % possible all: 98.3
Reflection
*PLUS
Highest resolution: 2.1 Å / Num. all: 73299 / Rmerge(I) obs: 0.079
Reflection shell
*PLUS
Highest resolution: 2.1 Å / % possible obs: 98.3 % / Rmerge(I) obs: 0.342

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→36.51 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.917 / SU B: 4.987 / SU ML: 0.136 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.214 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25561 3749 5.1 %RANDOM
Rwork0.19149 ---
obs0.19471 69488 100 %-
all-69488 --
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: 20.429 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20 Å2
2--0.03 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.1→36.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8085 0 144 810 9039
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0228312
X-RAY DIFFRACTIONr_angle_refined_deg1.1021.98811253
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.34831054
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.697151555
X-RAY DIFFRACTIONr_chiral_restr0.0730.21323
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026059
X-RAY DIFFRACTIONr_nbd_refined0.2710.33756
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2220.5945
X-RAY DIFFRACTIONr_metal_ion_refined0.0660.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.390
X-RAY DIFFRACTIONr_symmetry_hbond_refined1.0330.549
X-RAY DIFFRACTIONr_mcbond_it12.6921.55236
X-RAY DIFFRACTIONr_mcangle_it15.57328470
X-RAY DIFFRACTIONr_scbond_it23.57933076
X-RAY DIFFRACTIONr_scangle_it24.6324.52783
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.298 275
Rwork0.203 5062
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)
11.77330.15420.07341.0908-0.42861.60180.017-0.07310.01040.0719-0.0336-0.0221-0.02090.03210.01660.0791-0.01420.00460.0493-0.02840.016615.00465.81975.39
21.85540.97371.27384.32140.49832.3372-0.03590.0665-0.0409-0.17020.0704-0.11680.05230.2804-0.03450.08150.0260.02060.0559-0.02560.1137.49840.86980.836
31.3330.0632-0.24133.4598-2.13390.5953-0.14740.3328-0.0901-0.52530.19970.32590.2136-0.1449-0.05230.1712-0.0445-0.04330.1408-0.0280.08560.14159.61970.977
44.0378-0.33642.16362.07180.22484.0302-0.09880.54740.2998-0.2142-0.0101-0.0104-0.38230.19810.10880.1789-0.0048-0.01370.16770.06870.0986-13.67175.46950.049
52.32-0.1489-0.00571.7564-0.68362.24880.04280.02350.00690.0039-0.1283-0.1036-0.13140.08860.08550.2103-0.03860.00440.1022-0.01970.040616.651115.30273.449
63.40761.5911.98033.84250.10772.8914-0.0830.3436-0.5335-0.16140.1701-0.01420.00950.3135-0.08710.12860.02040.03030.0975-0.04960.22947.39291.14480.528
71.84040.0139-0.48833.0992-2.41580.8025-0.13840.3898-0.2325-0.49720.19920.32810.093-0.191-0.06080.2995-0.0432-0.0740.2319-0.05120.10741.248109.39369.757
83.91780.22662.32321.76010.8154.7722-0.32370.31130.3481-0.14690.07390.0143-0.71240.17630.24990.3667-0.0327-0.06990.14410.06050.1144-12.596124.79248.349
91.46730.02350.01480.949-0.36481.60520.0556-0.06670.05080.0341-0.0695-0.0484-0.0430.12540.01390.0868-0.02670.01170.0546-0.02430.016915.21915.1975.618
101.25450.31410.423.79680.28491.0379-0.04650.0104-0.0757-0.13880.0214-0.02830.01570.12930.02520.1174-0.00540.02030.067-0.02020.11627.343-9.82981.122
111.0074-0.2166-0.1132.7908-1.89131.4722-0.12540.3385-0.1428-0.4720.13160.21510.3096-0.1702-0.00620.1611-0.0452-0.02210.1309-0.03990.08210.328.69371.279
123.7043-0.08152.01312.07730.274.2404-0.15280.35230.2796-0.18380.0195-0.0392-0.48470.12050.13330.211-0.0074-0.01680.11590.05230.0751-13.69625.62250.717
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 - 353226 - 353
5X-RAY DIFFRACTION5BB3 - 883 - 88
6X-RAY DIFFRACTION6BB89 - 16089 - 160
7X-RAY DIFFRACTION7BB161 - 225161 - 225
8X-RAY DIFFRACTION8BB226 - 353226 - 353
9X-RAY DIFFRACTION9CC3 - 883 - 88
10X-RAY DIFFRACTION10CC89 - 16089 - 160
11X-RAY DIFFRACTION11CC161 - 225161 - 225
12X-RAY DIFFRACTION12CC226 - 353226 - 353
Refinement
*PLUS
Lowest resolution: 35 Å / Rfactor Rfree: 0.256 / Rfactor Rwork: 0.198
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_deg1.1

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