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- PDB-4r73: Structure of the periplasmic binding protein AfuA from Actinobaci... -

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Basic information

Entry
Database: PDB / ID: 4r73
TitleStructure of the periplasmic binding protein AfuA from Actinobacillus pleuropneumoniae (endogenous glucose-6-phosphate and mannose-6-phosphate bound)
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


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
6-O-phosphono-alpha-D-glucopyranose / 6-O-phosphono-alpha-D-mannopyranose / ABC-type Fe3+ transport system, periplasmic component
Similarity search - Component
Biological speciesActinobacillus pleuropneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsCalmettes, C. / Tang, C. / Sit, B. / 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 1.2Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _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

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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
B: ABC-type Fe3+ transport system, periplasmic component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,33514
Polymers70,7842
Non-polymers1,55112
Water13,025723
1
A: ABC-type Fe3+ transport system, periplasmic component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1677
Polymers35,3921
Non-polymers7756
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ABC-type Fe3+ transport system, periplasmic component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1677
Polymers35,3921
Non-polymers7756
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.530, 95.320, 152.100
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 35391.980 Da / Num. of mol.: 2 / 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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Sugars , 2 types, 4 molecules

#2: Sugar ChemComp-G6P / 6-O-phosphono-alpha-D-glucopyranose


Type: D-saccharide, alpha linking / Mass: 260.136 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
a-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Sugar ChemComp-M6P / 6-O-phosphono-alpha-D-mannopyranose


Type: D-saccharide, alpha linking / Mass: 260.136 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13O9P
IdentifierTypeProgram
a-D-Manp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 3 types, 731 molecules

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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 723 / 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: 2.23 Å3/Da / Density % sol: 44.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M magnesium chloride, 0.1 M Tris, pH 6.5, 25% 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→39.596 Å / Num. obs: 83626 / Biso Wilson estimate: 12.81 Å2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.6-1.67188.5
1.67-1.72194.1
1.72-1.78197.4
1.78-1.85198.6
1.85-1.92198.9
1.92-2.01199.3
2.01-2.11199.6
2.11-2.22199.8
2.22-2.36199.7
2.36-2.52199.8
2.52-2.72199.9
2.72-2.981100
2.98-3.331100
3.33-3.851100
3.85-4.711100
4.71-6.661100
6.66-39.5198.2

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.6→39.596 Å / SU ML: 0.14 / σ(F): 2 / Phase error: 18.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1942 4182 5 %
Rwork0.1606 --
obs0.1623 83626 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.24 Å2 / Biso mean: 17.0084 Å2 / Biso min: 3.09 Å2
Refinement stepCycle: LAST / Resolution: 1.6→39.596 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4963 0 92 723 5778
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145310
X-RAY DIFFRACTIONf_angle_d1.6417212
X-RAY DIFFRACTIONf_chiral_restr0.377801
X-RAY DIFFRACTIONf_plane_restr0.007923
X-RAY DIFFRACTIONf_dihedral_angle_d14.3742007
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.61820.24541260.21082382250889
1.6182-1.63720.18911260.18922402252892
1.6372-1.65720.20671310.18182490262194
1.6572-1.67820.25131360.17732580271697
1.6782-1.70020.20421340.17282554268898
1.7002-1.72350.23421380.17172612275099
1.7235-1.74820.22821400.175226752815100
1.7482-1.77430.22111380.165126092747100
1.7743-1.8020.21321390.170326462785100
1.802-1.83150.21151410.166426722813100
1.8315-1.86310.22331380.170726202758100
1.8631-1.8970.18971390.1626572796100
1.897-1.93350.24791400.168326452785100
1.9335-1.97290.19581410.164926772818100
1.9729-2.01580.19861390.16426402779100
2.0158-2.06270.2131400.162726662806100
2.0627-2.11430.18961390.159926462785100
2.1143-2.17150.1891410.159126802821100
2.1715-2.23540.19551390.157626322771100
2.2354-2.30750.19691420.160926992841100
2.3075-2.390.20631400.160826692809100
2.39-2.48560.19711400.164926642804100
2.4856-2.59870.22561420.166126882830100
2.5987-2.73570.19991420.170226952837100
2.7357-2.90710.21831430.163827132856100
2.9071-3.13140.2061410.166426952836100
3.1314-3.44640.17021430.15627202863100
3.4464-3.94470.15341450.137927442889100
3.9447-4.96840.16171460.137927692915100
4.9684-39.60860.17941530.16352903305699

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