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- PDB-4r72: Structure of the periplasmic binding protein AfuA from Actinobaci... -

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Basic information

Entry
Database: PDB / ID: 4r72
TitleStructure of the periplasmic binding protein AfuA from Actinobacillus pleuropneumoniae (apo form)
ComponentsABC-type Fe3+ transport system, periplasmic component
KeywordsTRANSPORT PROTEIN / ABC transporter / sugar transporter / glucose-6-phosphate / fructose-6-phosphate / sedoheptulose-7-phosphate
Function / homology
Function and homology information


thiamine binding / thiamine transport / thiamine pyrophosphate binding / outer membrane-bounded periplasmic space
Similarity search - Function
Bacterial extracellular solute-binding protein / Ferric binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / ABC-type Fe3+ transport system, periplasmic component
Similarity search - Component
Biological speciesActinobacillus pleuropneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSit, B. / Calmettes, C. / Moraes, T.F.
CitationJournal: Plos Pathog. / Year: 2015
Title: Active Transport of Phosphorylated Carbohydrates Promotes Intestinal Colonization and Transmission of a Bacterial Pathogen.
Authors: Sit, B. / Crowley, S.M. / Bhullar, K. / Lai, C.C. / Tang, C. / Hooda, Y. / Calmettes, C. / Khambati, H. / Ma, C. / Brumell, J.H. / Schryvers, A.B. / Vallance, B.A. / Moraes, T.F.
History
DepositionAug 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2015Group: Database references
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ABC-type Fe3+ transport system, periplasmic component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1169
Polymers35,3921
Non-polymers7248
Water7,656425
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.950, 80.820, 126.040
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-690-

HOH

21A-694-

HOH

31A-718-

HOH

41A-727-

HOH

51A-849-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ABC-type Fe3+ transport system, periplasmic component / AfuA


Mass: 35391.980 Da / Num. of mol.: 1 / Fragment: UNP residues 28-346
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinobacillus pleuropneumoniae (bacteria)
Gene: afuA, APL_1446 / Production host: Escherichia coli (E. coli) / References: UniProt: A3N294

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Non-polymers , 5 types, 433 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 425 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.08 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2 M magnesium chloride, 0.1 M MES/NaOH, pH 6.0, 27.5% PEG3350, 20% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX-300 / Detector: CCD
RadiationMonochromator: ACCEL/BRUKER double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.6→47.095 Å / Num. obs: 38225 / Biso Wilson estimate: 18.12 Å2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.6-1.65178.8
1.65-1.71190.7
1.71-1.77198.4
1.77-1.85199.9
1.85-1.931100
1.93-2.02199.5
2.02-2.13199.9
2.13-2.261100
2.26-2.421100
2.41-2.611100
2.61-2.86199.8
2.86-3.2199.9
3.2-3.691100
3.69-4.52199.9
4.52-6.4199.9
6.4-47.1199.9

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→47.095 Å / SU ML: 0.14 / σ(F): 1.36 / Phase error: 19.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1987 1912 5 %
Rwork0.1589 --
obs0.1609 38225 97.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.77 Å2 / Biso mean: 23.093 Å2 / Biso min: 9.22 Å2
Refinement stepCycle: LAST / Resolution: 1.6→47.095 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2473 0 46 425 2944
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122666
X-RAY DIFFRACTIONf_angle_d1.6353618
X-RAY DIFFRACTIONf_chiral_restr0.091400
X-RAY DIFFRACTIONf_plane_restr0.007463
X-RAY DIFFRACTIONf_dihedral_angle_d14.1021019
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.640.24821060.18252017212377
1.64-1.68440.24131210.19182301242287
1.6844-1.73390.23361330.17872511264495
1.7339-1.78990.25221390.178326472786100
1.7899-1.85390.22181380.170826312769100
1.8539-1.92810.21681410.17512663280499
1.9281-2.01590.20211380.162226262764100
2.0159-2.12220.21281400.156826522792100
2.1222-2.25510.1861400.158326792819100
2.2551-2.42920.23221400.164426502790100
2.4292-2.67370.18651410.16826822823100
2.6737-3.06050.21581420.165727002842100
3.0605-3.85560.18141440.146927292873100
3.8556-47.11510.16831490.144428252974100

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