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

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Basic information

Entry
Database: PDB / ID: 1oxv
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / IODIDE ION / Glucose import ATP-binding protein GlcV
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.95 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.ptnr1_label_seq_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_conn.ptnr2_label_seq_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
D: ABC transporter, ATP binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,91647
Polymers117,5023
Non-polymers6,41444
Water15,367853
1
A: ABC transporter, ATP binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,60118
Polymers39,1671
Non-polymers2,43417
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ABC transporter, ATP binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,22115
Polymers39,1671
Non-polymers2,05314
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: ABC transporter, ATP binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,09414
Polymers39,1671
Non-polymers1,92613
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.094, 148.776, 176.710
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: 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.: 38 / Source method: obtained synthetically / Formula: I
#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 853 / 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: 2.43 Å3/Da / Density % sol: 49.08 %
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: 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: 1.95→45 Å / Num. all: 94192 / Num. obs: 94192 / % possible obs: 95.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rsym value: 0.078 / Net I/σ(I): 12.2
Reflection shellResolution: 1.95→2 Å / Mean I/σ(I) obs: 2.7 / Rsym value: 0.35 / % possible all: 95.5
Reflection
*PLUS
Rmerge(I) obs: 0.078
Reflection shell
*PLUS
% possible obs: 95.5 % / Rmerge(I) obs: 0.35

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.95→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU B: 5.082 / SU ML: 0.148 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.164 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23976 4465 5.1 %RANDOM
Rwork0.18811 ---
obs0.19075 83301 100 %-
all-83301 --
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: 20.983 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7932 0 134 853 8919
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0228265
X-RAY DIFFRACTIONr_bond_other_d00.028023
X-RAY DIFFRACTIONr_angle_refined_deg1.251.99211194
X-RAY DIFFRACTIONr_angle_other_deg1.275318636
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.43731056
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.507151559
X-RAY DIFFRACTIONr_chiral_restr0.1090.21319
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.029041
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021580
X-RAY DIFFRACTIONr_nbd_refined0.3370.31824
X-RAY DIFFRACTIONr_nbd_other0.30.38114
X-RAY DIFFRACTIONr_nbtor_other1.0750.529
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2840.5791
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.330.518
X-RAY DIFFRACTIONr_metal_ion_refined0.0330.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3740.334
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2970.366
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3230.546
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it4.7121.55221
X-RAY DIFFRACTIONr_mcangle_it6.60928440
X-RAY DIFFRACTIONr_scbond_it10.08233044
X-RAY DIFFRACTIONr_scangle_it13.1564.52754
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.276 346
Rwork0.218 5995
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)
11.73970.0807-0.52951.148-0.53532.41070.0023-0.0221-0.01460.0715-0.0383-0.0514-0.04370.04270.03610.0337-0.0137-0.00660.0487-0.0130.00714.66465.61175.583
20.88740.77581.26145.11860.54392.5855-0.01540.0947-0.1473-0.22770.079-0.04690.09270.2832-0.06350.08580.03240.01050.046-0.05450.1697.1440.80481.023
31.0233-0.29330.19743.9667-2.89431.5944-0.05960.2636-0.1084-0.62520.24350.40240.4119-0.1916-0.1840.1672-0.052-0.04510.106-0.02760.0799-0.15259.15471.029
44.341-0.13442.53272.3103-0.01063.7848-0.18840.57030.2529-0.2150.0882-0.0636-0.31590.27590.10020.1289-0.0417-0.00220.13940.07150.0956-13.67175.03650.306
52.894-0.0457-0.72971.5601-0.22042.9389-0.01510.11-0.00610.0378-0.0822-0.0885-0.0809-0.01440.09720.1469-0.032-0.0130.0818-0.01210.053815.941114.99173.876
66.24340.91582.92484.47150.13223.5566-0.05080.6142-0.8679-0.29150.2923-0.0691-0.04620.3947-0.24150.11470.00350.02330.0809-0.11280.30156.9891.03280.722
71.2922-0.59280.76232.8934-2.70132.1331-0.07430.1721-0.1601-0.55060.1630.33910.3014-0.3779-0.08870.2909-0.0419-0.04110.2049-0.07150.13030.457109.23270.006
85.18110.35352.83722.590.27513.9892-0.3260.4590.395-0.16860.1432-0.0409-0.55880.25910.18280.2867-0.0499-0.06480.11240.05720.1493-12.915124.35348.667
91.78960.1645-0.41621.1217-0.54071.74780.0354-0.06780.02410.0528-0.0718-0.0554-0.03640.120.03640.0482-0.02170.00320.0433-0.00780.017614.67114.99975.972
101.29760.52020.0885.27420.15871.3891-0.10550.0301-0.1451-0.27810.01820.04170.00340.10560.08720.11160.00650.01670.0375-0.03740.16866.909-9.79781.296
110.7707-0.40980.22363.1659-2.29721.3943-0.04750.1924-0.0794-0.49230.16450.33170.3149-0.172-0.11690.1459-0.0426-0.02280.0692-0.01720.0615-0.1078.73871.474
123.7994-0.32912.0862.4158-0.05833.4966-0.19910.48760.2592-0.19030.0492-0.0497-0.38940.23940.150.1617-0.0311-0.01870.11180.06820.0793-13.825.20650.85
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 DIFFRACTION5BB1 - 881 - 88
6X-RAY DIFFRACTION6BB89 - 16089 - 160
7X-RAY DIFFRACTION7BB161 - 225161 - 225
8X-RAY DIFFRACTION8BB226 - 353226 - 353
9X-RAY DIFFRACTION9DC1 - 881 - 88
10X-RAY DIFFRACTION10DC89 - 16089 - 160
11X-RAY DIFFRACTION11DC161 - 225161 - 225
12X-RAY DIFFRACTION12DC226 - 353226 - 353
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.188
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_deg1.25

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