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- PDB-5dte: Crystal Structure of an ABC transporter periplasmic solute bindin... -

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Basic information

Entry
Database: PDB / ID: 5dte
TitleCrystal Structure of an ABC transporter periplasmic solute binding protein (IPR025997) from Actinobacillus succinogenes 130z(Asuc_0081, TARGET EFI-511065) with bound D-allose
ComponentsMonosaccharide-transporting ATPase
KeywordsTRANSPORT PROTEIN / Solute Binding Protein / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics
Function / homology
Function and homology information


monosaccharide-transporting ATPase / hydrolase activity
Similarity search - Function
Periplasmic binding protein / Periplasmic binding protein domain / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
beta-D-allopyranose / Monosaccharide-transporting ATPase
Similarity search - Component
Biological speciesActinobacillus succinogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsYadava, U. / Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Koss, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. ...Yadava, U. / Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Koss, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Love, J. / Seidel, R.D. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be published
Title: Crystal Structure of an ABC transporter periplasmic solute binding protein (IPR025997) from Actinobacillus succinogenes 130z(Asuc_0081, TARGET EFI-511065) with bound D-allose
Authors: Yadava, U. / Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Koss, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, ...Authors: Yadava, U. / Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Koss, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Love, J. / Seidel, R.D. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionSep 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2017Group: Atomic model / Derived calculations / Category: atom_site / pdbx_struct_oper_list
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id / _pdbx_struct_oper_list.symmetry_operation
Revision 2.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Monosaccharide-transporting ATPase
B: Monosaccharide-transporting ATPase
C: Monosaccharide-transporting ATPase
D: Monosaccharide-transporting ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,5378
Polymers134,8174
Non-polymers7214
Water1,02757
1
A: Monosaccharide-transporting ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8842
Polymers33,7041
Non-polymers1801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Monosaccharide-transporting ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8842
Polymers33,7041
Non-polymers1801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Monosaccharide-transporting ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8842
Polymers33,7041
Non-polymers1801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Monosaccharide-transporting ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8842
Polymers33,7041
Non-polymers1801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.190, 63.218, 71.201
Angle α, β, γ (deg.)101.130, 103.290, 91.350
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Monosaccharide-transporting ATPase /


Mass: 33704.191 Da / Num. of mol.: 4 / Fragment: Solute binding protein
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinobacillus succinogenes (strain ATCC 55618 / 130Z) (bacteria)
Strain: ATCC 55618 / 130Z / Gene: Asuc_0081 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A6VKG5, monosaccharide-transporting ATPase
#2: Sugar
ChemComp-ALL / beta-D-allopyranose / beta-D-allose / D-allose / allose / D-ALLOPYRANOSE / Allose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DAllpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-allopyranoseCOMMON NAMEGMML 1.0
b-D-AllpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
AllSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 1.98 Å3/Da / Density % sol: 37.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein (10 mM D-allose, 10 mM HEPES pH 7.5, 5 mM DTT); Reservoir (1.0 M Lithium chloride, 0.1 M sodium citrate:HCl pH 4.0, 20% (w/v) PEG 6000); Cryoprotection (20% Ethylene glycol, 80% Reservoir)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Aug 15, 2015 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.29→42 Å / Num. obs: 28967 / % possible obs: 63.1 % / Redundancy: 3.4 % / Biso Wilson estimate: 30.8 Å2 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.072 / Rrim(I) all: 0.133 / Χ2: 0.903 / Net I/av σ(I): 10.257 / Net I/σ(I): 7.5 / Num. measured all: 98224
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.29-2.332.42060.4450.8210.7059.2
2.33-2.372.72980.6070.5610.85512.70.828
2.37-2.422.93830.5540.5440.82716.80.8020.974
2.42-2.473.14510.5750.5710.80719.90.872
2.47-2.523.25680.6390.470.80124.70.7210.864
2.52-2.583.26940.6880.3810.77730.20.5840.7
2.58-2.643.38420.7560.3570.87136.60.5620.668
2.64-2.713.49620.8480.2860.83742.40.450.535
2.71-2.793.411730.8410.2510.8951.30.3990.473
2.79-2.893.314910.9120.2040.93463.90.3210.382
2.89-2.993.218860.9370.1780.99182.60.2720.326
2.99-3.113.322080.9470.1450.9396.50.2260.27
3.11-3.253.422330.9480.1220.97296.70.1930.229
3.25-3.423.422130.9680.0911.01496.90.1440.171
3.42-3.633.422400.980.0721.01296.70.1140.136
3.63-3.913.522140.9860.0621.05796.70.0990.118
3.91-4.313.522200.9890.0480.903970.0760.09
4.31-4.933.522030.990.0420.8495.80.0680.08
4.93-6.213.622260.9910.0440.72296.60.0710.083
6.21-423.622560.9920.0370.77298.60.060.071

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IOY

2ioy


Resolution: 2.7→33.147 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 31.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2752 1180 4.76 %
Rwork0.1644 23585 -
obs0.1698 24765 87.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.89 Å2 / Biso mean: 28.6742 Å2 / Biso min: 0 Å2
Refinement stepCycle: final / Resolution: 2.7→33.147 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8631 0 48 61 8740
Biso mean--27.52 14.21 -
Num. residues----1140
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098794
X-RAY DIFFRACTIONf_angle_d1.19611917
X-RAY DIFFRACTIONf_chiral_restr0.0451404
X-RAY DIFFRACTIONf_plane_restr0.0061560
X-RAY DIFFRACTIONf_dihedral_angle_d16.0023265
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.82280.409820.22531670175249
2.8228-2.97160.35741280.22972380250871
2.9716-3.15760.35511490.21183236338596
3.1576-3.40120.3171600.19263268342897
3.4012-3.7430.28611750.16583261343697
3.743-4.28370.25231340.13823261339596
4.2837-5.39320.2341930.12813216340996
5.3932-33.14920.21061590.14773293345297
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)
10.02470.04350.01410.20420.12980.1030.0132-0.0267-0.04470.03920.0451-0.06380.19780.06960.04440.1194-0.00520.0150.12790.00660.043113.6271-7.3978-2.3107
20.01010.0208-0.02870.069-0.06370.07830.0142-0.20760.067-0.0518-0.1122-0.06990.0056-0.0672-0.01480.1707-0.0497-0.07330.1847-0.02840.207115.00745.70385.2844
30.0789-0.0495-0.03530.20350.0180.0181-0.03230.00470.06290.10910.05730.002-0.0723-0.0147-0.00880.15120.00790.04950.1468-0.03130.0964-2.1989.0531-2.9633
40.2749-0.1045-0.10430.1673-0.03880.1444-0.0408-0.13150.11720.1660.0706-0.0024-0.0901-0.11830.00220.12660.014-0.02110.1434-0.0030.0928-14.1262.32794.9437
50.1160.03620.01280.15910.14580.14080.06430.0515-0.02270.03110.0971-0.03820.0155-0.03870.04570.13840.0387-0.06130.12280.0360.1592-17.4804-4.77921.016
60.11780.06570.01970.2983-0.07990.1001-0.05620.04160.0050.0470.0054-0.07840.0571-0.0951-0.14950.0741-0.0452-0.01620.1124-0.01790.0963-13.573-4.4859-7.716
70.05260.0238-0.01440.2350.00570.0695-0.00320.00160.0220.03080.10170.06880.04830.07350.00850.29970.03250.04780.13830.02250.095113.66531.9859-10.7881
80.0989-0.08680.04020.0789-0.03920.01810.00320.22610.0641-0.0583-0.0924-0.1329-0.04540.0104-0.06030.09280.0028-0.06380.19150.01980.22771.59585.1575-13.0802
90.0192-0.02290.00430.0402-0.04790.1971-0.13070.00940.12160.18620.09240.0045-0.0757-0.211-0.00920.1912-0.0250.01630.1810.01530.20659.0154-7.293638.0875
100.0236-0.060.02420.1518-0.06470.0298-0.10790.0430.10470.0384-0.0371-0.2386-0.1898-0.0899-0.02280.15750.00510.02430.1345-0.02470.172315.6395-8.530529.2748
110.0322-0.0154-0.02440.00620.00550.10740.06860.0532-0.0953-0.2091-0.0766-0.15380.02380.0055-0.00130.14680.04110.02690.08340.0250.184614.917-20.963525.5457
120.0811-0.0275-0.00780.09880.16520.2838-0.0567-0.046-0.00640.1964-0.0091-0.00910.0714-0.0502-0.01150.1449-0.004-0.04730.05330.00940.1248-2.5189-25.414532.4976
130.0884-0.1452-0.00310.3404-0.08540.07030.05560.1109-0.0383-0.1905-0.04290.03430.0537-0.049-0.01320.11450.0061-0.01730.1202-0.02110.045-13.2376-22.554624.7704
140.0472-0.00940.01370.05490.00630.0059-0.02550.1519-0.028-0.0242-0.0113-0.03620.0425-0.071900.1081-0.01320.00940.15640.01860.1103-18.0966-11.587826.7614
150.03210.03610.01440.0624-0.03630.1048-0.0170.0004-0.06760.05420.043-0.02560.12110.00370.00250.1018-0.0045-0.01110.085-0.0110.1249-1.6621-14.517640.2209
160.63590.0640.16450.29210.02620.13130.0278-0.0829-0.0160.0969-0.0208-0.04810.11580.0738-0.03050.07850.05620.02940.06440.03950.18180.201-21.482442.742
170.18420.03510.06380.16770.1730.1618-0.02430.0144-0.06660.0382-0.0403-0.00710.0291-0.0359-0.00030.06410.00340.00330.1240.01190.1158-20.661512.251729.0101
180.11210.12360.04470.13340.04220.1475-0.0626-0.0159-0.07320.03340.0878-0.0184-0.00510.07140.2569-0.00470.0692-0.05450.00530.04810.0869-0.942614.396532.4272
190.16570.0159-0.00870.01950.0590.2338-0.0218-0.06880.066-0.03950.0084-0.09190.0138-0.0585-0.00070.10290.00620.00590.0935-0.01570.0935-18.8978-29.9015-1.072
200.23420.0060.14960.14790.01070.21080.03040.05630.0224-0.01840.0096-0.0158-0.0125-0.026-00.1109-0.01870.0090.09530.0050.09591.131-30.5717-2.8067
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 28 through 93 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 94 through 128 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 129 through 154 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 155 through 215 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 216 through 239 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 240 through 273 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 274 through 289 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 290 through 313 )A0
9X-RAY DIFFRACTION9chain 'B' and (resid 27 through 56 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 57 through 93 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 94 through 128 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 129 through 154 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 155 through 201 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 202 through 254 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 255 through 289 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 290 through 313 )B0
17X-RAY DIFFRACTION17chain 'C' and (resid 28 through 154 )C0
18X-RAY DIFFRACTION18chain 'C' and (resid 155 through 313 )C0
19X-RAY DIFFRACTION19chain 'D' and (resid 28 through 154 )D0
20X-RAY DIFFRACTION20chain 'D' and (resid 155 through 313 )D0

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