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Basic information

Entry
Database: PDB / ID: 3ooa
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: 2.04 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)93,75225
Polymers91,5582
Non-polymers2,19423
Water16,808933
1
A: ABC transporter binding protein AcbH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,92813
Polymers45,7791
Non-polymers1,14912
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)46,82412
Polymers45,7791
Non-polymers1,04511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.250, 66.117, 177.709
Angle α, β, γ (deg.)90.00, 89.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ABC transporter binding protein AcbH


Mass: 45779.234 Da / Num. of mol.: 2 / Fragment: residue in UNP 39-433 / Mutation: T10M, R362A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinoplanes (bacteria) / Strain: SE50/110 / Gene: AcbH / Plasmid: pAL56, 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.: 19 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 933 / 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: 2.52 Å3/Da / Density % sol: 51.19 %
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: 2.04→33.75 Å / Num. obs: 57305 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 23.568 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 9.48
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
2.04-2.090.7470.5382.211621427741190.65596.3
2.09-2.150.6230.4492.611726419040640.54797
2.15-2.210.5010.3713.211520404739420.45197.4
2.21-2.280.4370.333.611716398238900.39997.7
2.28-2.360.3770.2934.111229375436640.35497.6
2.36-2.440.3080.2434.911488374536720.29398.1
2.44-2.530.280.2215.411225353134850.26598.7
2.53-2.630.2250.1846.611298350334500.2298.5
2.63-2.750.1830.1567.810910327332260.18598.6
2.75-2.890.1620.1329.110799315031200.15799
2.89-3.040.1220.10611.210437300929810.12699.1
3.04-3.230.0930.08513.810193284628210.199.1
3.23-3.450.070.0716.69658265626480.08299.7
3.45-3.720.0580.06118.79209250525000.07299.8
3.72-4.080.0490.05420.78499230523000.06399.8
4.08-4.560.0480.05321.57716209020860.06299.8
4.56-5.270.0470.0520.86888183718350.05899.9
5.27-6.450.0520.05118.96024160516050.06100
6.45-9.120.0360.03622.54456120812080.043100
9.120.0270.02625.324027076890.03197.5

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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: 2.04→33.75 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.912 / WRfactor Rfree: 0.2088 / WRfactor Rwork: 0.1544 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8685 / SU B: 4.044 / SU ML: 0.11 / SU R Cruickshank DPI: 0.1844 / SU Rfree: 0.1703 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2255 2866 5 %RANDOM
Rwork0.1675 ---
obs0.1704 54440 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: 74.99 Å2 / Biso mean: 17.6948 Å2 / Biso min: 3.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.38 Å20 Å2-0.15 Å2
2--0.19 Å20 Å2
3---1.18 Å2
Refinement stepCycle: LAST / Resolution: 2.04→33.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6158 0 119 933 7210
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0226416
X-RAY DIFFRACTIONr_angle_refined_deg1.0471.9528740
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2985788
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.05225.548292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.55615990
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9261512
X-RAY DIFFRACTIONr_chiral_restr0.090.2928
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0214904
X-RAY DIFFRACTIONr_mcbond_it1.0831.53938
X-RAY DIFFRACTIONr_mcangle_it1.74226326
X-RAY DIFFRACTIONr_scbond_it3.2632478
X-RAY DIFFRACTIONr_scangle_it4.6954.52414
LS refinement shellResolution: 2.04→2.093 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 206 -
Rwork0.217 3901 -
all-4107 -
obs--100 %

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