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Basic information

Entry
Database: PDB / ID: 3oo6
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 / xylan catabolic process / maltose binding / 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
beta-D-galactopyranose / ABC transporter binding protein AcbH
Similarity search - Component
Biological speciesActinoplanes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / 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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Mar 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ABC transporter binding protein AcbH
B: ABC transporter binding protein AcbH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,2836
Polymers91,7312
Non-polymers5524
Water11,836657
1
A: ABC transporter binding protein AcbH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0462
Polymers45,8651
Non-polymers1801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ABC transporter binding protein AcbH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2384
Polymers45,8651
Non-polymers3723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.835, 98.812, 95.732
Angle α, β, γ (deg.)90.000, 95.040, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ABC transporter binding protein AcbH


Mass: 45865.352 Da / Num. of mol.: 2 / Fragment: residue in UNP 39-433 / Mutation: T10M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinoplanes (bacteria) / Strain: SE50/110 / Gene: AcbH / Plasmid: pAL8, pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 / References: UniProt: Q27GR2
#2: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 657 / 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: 2.46 Å3/Da / Density % sol: 49.94 % / Mosaicity: 0.419 °
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: Aug 23, 2007 / 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: 2.15→50 Å / Num. obs: 44711 / % possible obs: 93.1 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.084 / Χ2: 0.908 / Net I/σ(I): 6.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.15-2.232.50.23439540.856183.2
2.23-2.322.80.20841220.776186.9
2.32-2.422.80.19142230.797187.9
2.42-2.552.90.16942890.817189.3
2.55-2.712.90.14843560.88191.3
2.71-2.922.90.11645440.893194.8
2.92-3.212.90.08747491.021198.6
3.21-3.683.10.06448091.086199.8
3.68-4.633.20.0547921.064199.9
4.63-503.20.04548730.789199.2

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Processing

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

Resolution: 2.15→34.31 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.903 / WRfactor Rfree: 0.2299 / WRfactor Rwork: 0.1715 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8094 / SU B: 5.15 / SU ML: 0.137 / SU R Cruickshank DPI: 0.2812 / SU Rfree: 0.2253 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2509 2235 5 %RANDOM
Rwork0.1877 ---
obs0.1909 44697 92.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 47.57 Å2 / Biso mean: 13.203 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--1.72 Å20 Å2-0.43 Å2
2--2.14 Å20 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 2.15→34.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6100 0 34 657 6791
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226308
X-RAY DIFFRACTIONr_angle_refined_deg0.9311.9428592
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7765782
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.62725.411292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.86115990
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.6791514
X-RAY DIFFRACTIONr_chiral_restr0.0830.2928
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214874
X-RAY DIFFRACTIONr_mcbond_it0.8171.53894
X-RAY DIFFRACTIONr_mcangle_it1.37226258
X-RAY DIFFRACTIONr_scbond_it2.60232414
X-RAY DIFFRACTIONr_scangle_it3.7634.52332
LS refinement shellResolution: 2.152→2.208 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 131 -
Rwork0.199 2648 -
all-2779 -
obs--79.54 %

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