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- PDB-4zjp: Structure of an ABC-Transporter Solute Binding Protein (SBP_IPR02... -

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Entry
Database: PDB / ID: 4zjp
TitleStructure of an ABC-Transporter Solute Binding Protein (SBP_IPR025997) from Actinobacillus Succinogenes (Asuc_0197, TARGET EFI-511067) with bound beta-D-ribopyranose
ComponentsMonosaccharide-transporting ATPase
KeywordsSUGAR BINDING PROTEIN / Solute binding protein / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics
Function / homology
Function and homology information


monosaccharide-transporting ATPase / ABC-type monosaccharide transporter activity / 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-ribopyranose / Monosaccharide-transporting ATPase
Similarity search - Component
Biological speciesActinobacillus succinogenes (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsYadava, U. / Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Wasserman, S.R. / Attonito, J.D. / Glenn, A.S. / Chamala, S. ...Yadava, U. / Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Wasserman, S.R. / Attonito, J.D. / Glenn, A.S. / 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: Structure of an ABC-Transporter Solute Binding Protein (SBP_IPR025997) from Actinobacillus Succinogenes (Asuc_0197, TARGET EFI-511067) with bound beta-D-ribopyranose
Authors: Yadava, U. / Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Wasserman, S.R. / Attonito, J.D. / Glenn, A.S. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Love, J. / ...Authors: Yadava, U. / Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Wasserman, S.R. / Attonito, J.D. / Glenn, A.S. / 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
DepositionApr 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp / entity ...chem_comp / entity / entity_src_gen / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / refine_hist / struct_keywords / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _entity_src_gen.pdbx_alt_source_flag / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.d_res_low / _struct_keywords.text
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Sep 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
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Monosaccharide-transporting ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0373
Polymers30,8241
Non-polymers2122
Water6,341352
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area540 Å2
ΔGint8 kcal/mol
Surface area11590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.261, 37.416, 48.165
Angle α, β, γ (deg.)95.200, 101.030, 97.090
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Monosaccharide-transporting ATPase


Mass: 30824.338 Da / Num. of mol.: 1 / Fragment: UNP residues 24-292
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinobacillus succinogenes (strain ATCC 55618 / 130Z) (bacteria)
Strain: ATCC 55618 / 130Z / Gene: Asuc_0197 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A6VKT0, monosaccharide-transporting ATPase
#2: Sugar ChemComp-RIP / beta-D-ribopyranose / beta-D-ribose / D-ribose / ribose / RIBOSE(PYRANOSE FORM)


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
DRibpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-ribopyranoseCOMMON NAMEGMML 1.0
b-D-RibpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
RibSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / 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: 2.05 Å3/Da / Density % sol: 40.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein (40 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 10 mM D-ribose); Reservoir (22.7 %(w/v) PEG 3350, 0.1M BisTris pH 8.0); Cryoprotection (80% reservoir,20% ethylene glycol)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54056 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 22, 2015 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54056 Å / Relative weight: 1
ReflectionResolution: 1.63→20 Å / Num. obs: 26483 / % possible obs: 87.1 % / Redundancy: 2.6 % / Biso Wilson estimate: 15.37 Å2 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.034 / Rrim(I) all: 0.057 / Χ2: 2.926 / Net I/av σ(I): 39.482 / Net I/σ(I): 30 / Num. measured all: 69277
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.63-1.662.60.16512390.9520.1180.2042.89881.5
1.66-1.692.60.15912470.9490.1150.1972.87983.2
1.69-1.722.60.13513010.9660.0980.1672.72583.6
1.72-1.762.70.12112840.9740.0870.152.83485.8
1.76-1.792.70.10512780.9790.0760.132.61384.1
1.79-1.842.60.09712940.9820.0710.1212.86685.1
1.84-1.882.60.08313230.9870.060.1032.91986.1
1.88-1.932.60.07412960.9870.0540.0922.80285.3
1.93-1.992.60.0712990.9890.0510.0873.12986.4
1.99-2.052.60.06213170.990.0450.0773.04587.6
2.05-2.132.60.05613560.9920.0410.0693.06186.9
2.13-2.212.60.0513310.9930.0370.0632.98688.1
2.21-2.312.60.04713330.9930.0350.0592.95687.8
2.31-2.432.60.04313600.9940.0310.0532.68588.9
2.43-2.592.60.04313540.9950.0310.0532.7589.6
2.59-2.792.60.03913720.9950.0290.0492.62490.1
2.79-3.062.60.03913860.9950.0280.0482.72191
3.06-3.512.60.03913650.9950.0290.0482.94190.4
3.51-4.412.60.03913900.9950.0290.0483.28190.9
4.41-202.50.04213580.9940.0320.0533.86889.3

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DRI

2dri


Resolution: 1.63→20 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 18.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1849 1289 4.87 %
Rwork0.1415 25194 -
obs0.1436 26483 86.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.54 Å2 / Biso mean: 19.9305 Å2 / Biso min: 7.05 Å2
Refinement stepCycle: final / Resolution: 1.63→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1971 0 20 352 2343
Biso mean--24.94 33.28 -
Num. residues----270
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062063
X-RAY DIFFRACTIONf_angle_d0.9532795
X-RAY DIFFRACTIONf_chiral_restr0.038341
X-RAY DIFFRACTIONf_plane_restr0.004367
X-RAY DIFFRACTIONf_dihedral_angle_d14.057771
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.63-1.69530.22271370.1662552268980
1.6953-1.77240.21261510.15522729288084
1.7724-1.86580.20131510.14832722287385
1.8658-1.98250.19871270.14522812293986
1.9825-2.13540.18011440.14612807295187
2.1354-2.350.19421310.14672849298088
2.35-2.68930.1911200.15392924304489
2.6893-3.38540.20691660.14212894306090
3.3854-19.61170.1491620.1232905306790
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)
11.5239-0.35090.71911.6743-0.25841.9291-0.0577-0.04180.1957-0.10070.08090.1723-0.1742-0.23570.00210.11330.006-0.00250.1385-0.04060.137519.57816.883440.262
21.63710.3016-0.00873.0164-1.08872.49510.00850.06650.0005-0.14010.06630.18960.0477-0.3741-0.07580.0941-0.0097-0.00280.166-0.02150.143214.2161-0.582734.1304
32.7404-0.36851.21095.5682-3.68955.0475-0.06310.08190.0416-0.14430.17680.4168-0.1623-0.1847-0.06410.1012-0.01910.00590.1063-0.01380.095420.7028-1.017332.9879
43.36440.83672.24592.73451.81593.90090.00270.1555-0.0575-0.1887-0.12080.191-0.0505-0.17560.12180.1157-0.0108-00.1085-0.02040.094122.5014-3.194526.9342
50.2901-0.30610.78610.7823-0.82161.6352-0.03450.0320.0125-0.0119-0.0459-0.10560.00230.16890.07630.0899-0.00380.01910.1286-0.00850.117434.5797-9.919348.6633
61.0503-0.18990.43371.6654-0.48381.27920.03540.0356-0.1274-0.0321-0.00750.05710.08450.0147-0.01770.0938-0.01570.01390.1054-0.02660.112429.8843-17.36854.0956
70.61070.61390.25592.0236-1.66572.70040.0346-0.0479-0.05560.1142-0.10.0255-0.04250.0380.05840.0904-0.0280.02330.1303-0.00420.107826.6255-14.14661.052
81.47911.0258-0.58112.2059-1.12052.33260.0417-0.29060.06910.1491-0.08780.0621-0.06680.0410.04080.0964-0.01290.00360.1562-0.02650.092128.5228-4.852161.3502
91.5173-0.4571.14121.9751-1.68414.5212-0.00450.06750.18050.0289-0.0916-0.1245-0.35990.35860.11990.1003-0.06170.00640.1081-0.02540.142232.41536.352940.1478
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 23 through 53 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 54 through 78 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 79 through 92 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 93 through 111 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 112 through 158 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 159 through 202 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 203 through 226 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 227 through 258 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 259 through 292 )A0

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