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Basic information

Entry
Database: PDB / ID: 3oo8
TitleCrystal structures and biochemical characterization of the bacterial solute receptor AcbH reveal an unprecedented exclusive substrate preference for b-D-galactopyranose
ComponentsABC transporter binding protein AcbH
KeywordsSUGAR BINDING PROTEIN / class 2 SBP fold / ABC transporter extracellular solute binding protein / D-galactose Binding
Function / homology
Function and homology information


hydrolase activity, acting on glycosyl bonds / maltose binding / xylan catabolic process / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing
Similarity search - Function
Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ABC transporter binding protein AcbH
Similarity search - Component
Biological speciesActinoplanes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsVahedi-Faridi, A. / Bulut, H. / Licht, A.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Crystal structures of the bacterial solute receptor AcbH displaying an exclusive substrate preference for beta-D-galactopyranose
Authors: Licht, A. / Bulut, H. / Scheffel, F. / Daumke, O. / Wehmeier, U.F. / Saenger, W. / Schneider, E. / Vahedi-Faridi, A.
History
DepositionAug 30, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 26, 2014Group: Database references
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ABC transporter binding protein AcbH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6289
Polymers45,8791
Non-polymers7498
Water8,017445
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.507, 88.910, 102.678
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 binding protein AcbH


Mass: 45879.379 Da / Num. of mol.: 1 / Fragment: residue in UNP 39-433 / Mutation: T10M, D361E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinoplanes (bacteria) / Strain: SE50/110 / Gene: AcbH / Plasmid: pAL54, pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 / References: UniProt: Q27GR2
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / 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: 1.97 Å3/Da / Density % sol: 37.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 2.2M (NH4)2SO4, 100mM citric acid, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 17, 2010 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.53→33.61 Å / Num. obs: 55416 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 22.253 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 16.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.53-1.570.6430.6922.522052407140440.76499.3
1.57-1.610.5160.5573.222034391638980.61399.5
1.61-1.660.4290.4773.822390385038380.52399.7
1.66-1.710.3310.384.722441373837330.41699.9
1.71-1.770.2730.3185.722298360736040.34799.9
1.77-1.830.1970.2447.522065350134990.26799.9
1.83-1.90.1630.2921810340934080.218100
1.9-1.980.1250.15911.221066327432740.173100
1.98-2.060.0880.11914.620227311831170.13100
2.06-2.160.0690.09617.419478300630040.10599.9
2.16-2.280.0570.08220.518507286528650.089100
2.28-2.420.0510.07122.817454270527050.077100
2.42-2.590.0440.06525.216439255725560.07100
2.59-2.790.0370.05628.215406239823980.061100
2.79-3.060.0310.04832.514118221422140.053100
3.06-3.420.0230.03938.112718201520150.042100
3.42-3.950.0180.03442.311195179617960.037100
3.95-4.840.0160.03245.59395152015200.035100
4.84-6.840.0160.02943.87398122112200.03299.9

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: model from SeMet SAD phasing

Resolution: 1.6→33.61 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.762 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20986 2430 5 %RANDOM
Rwork0.16683 ---
obs0.16895 46164 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.339 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.6→33.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3051 0 45 445 3541
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223180
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4881.9464322
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4665391
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.20125.442147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.86215496
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.703157
X-RAY DIFFRACTIONr_chiral_restr0.1170.2458
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212445
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4991.51950
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.27123133
X-RAY DIFFRACTIONr_scbond_it3.58631230
X-RAY DIFFRACTIONr_scangle_it5.3484.51189
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 177 -
Rwork0.239 3365 -
obs--100 %

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