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Basic information

Entry
Database: PDB / ID: 3oo9
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
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: 1.76 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
B: ABC transporter binding protein AcbH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,04427
Polymers91,6752
Non-polymers2,37025
Water18,0871004
1
A: ABC transporter binding protein AcbH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,88612
Polymers45,8371
Non-polymers1,04911
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)47,15815
Polymers45,8371
Non-polymers1,32114
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.250, 65.760, 177.720
Angle α, β, γ (deg.)90.00, 90.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ABC transporter binding protein AcbH


Mass: 45837.336 Da / Num. of mol.: 2 / Fragment: residue in UNP 39-433 / Mutation: T10M, R362K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinoplanes (bacteria) / Strain: SE50/110 / Gene: AcbH / Plasmid: pAL55, 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.: 17 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1004 / 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: 2.5 Å3/Da / Density % sol: 50.87 %
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: 1.76→33.71 Å / Num. obs: 84900 / % possible obs: 94.4 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Biso Wilson estimate: 20.134 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 8.78
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.76-1.810.820.5531.813578663358810.6988.7
1.81-1.860.6510.4452.213634648158060.55489.6
1.86-1.910.5860.4062.513589624557030.50591.3
1.91-1.970.4390.3113.213673612856510.38792.2
1.97-2.030.3660.2533.913605584654400.31393.1
2.03-2.10.2790.2034.913710573153810.2593.9
2.1-2.180.2440.1735.813759559352920.21494.6
2.18-2.270.2040.1526.713571525550230.18795.6
2.27-2.370.180.1367.513579507348990.16796.6
2.37-2.490.1570.128.413425489247290.14796.7
2.49-2.620.1390.119.413313469045300.13596.6
2.62-2.780.1110.0921112819435442460.11297.5
2.78-2.970.0960.08312.412549413440500.198
2.97-3.210.0750.0715.312062386437860.08398
3.21-3.520.0590.0618.211266355634600.07297.3
3.52-3.940.0470.05120.610320323131450.0697.3
3.94-4.540.040.04522.49053282627520.05397.4
4.54-5.570.0390.04422.17963243623530.05296.6
5.57-7.870.040.042216107188817990.0595.3
7.870.0240.02625322110619740.03191.8

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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: 1.76→33.71 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.1808 / WRfactor Rwork: 0.1426 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8906 / SU B: 2.217 / SU ML: 0.069 / SU R Cruickshank DPI: 0.1047 / SU Rfree: 0.1051 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1948 4245 5 %RANDOM
Rwork0.155 ---
obs0.157 84899 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 96.69 Å2 / Biso mean: 14.5202 Å2 / Biso min: 3.45 Å2
Baniso -1Baniso -2Baniso -3
1--0.99 Å20 Å2-0.3 Å2
2--0.61 Å20 Å2
3---0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.76→33.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6166 0 133 1004 7303
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0226454
X-RAY DIFFRACTIONr_angle_refined_deg1.3591.9548785
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6425794
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.60125.548292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.172151001
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0441512
X-RAY DIFFRACTIONr_chiral_restr0.1140.2931
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214924
X-RAY DIFFRACTIONr_mcbond_it1.4051.53953
X-RAY DIFFRACTIONr_mcangle_it2.11526356
X-RAY DIFFRACTIONr_scbond_it3.65132501
X-RAY DIFFRACTIONr_scangle_it5.4074.52428
LS refinement shellResolution: 1.76→1.806 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 293 -
Rwork0.24 5569 -
all-5862 -
obs--100 %

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