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- PDB-4r74: Structure of the periplasmic binding protein AfuA from Actinobaci... -

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Basic information

Entry
Database: PDB / ID: 4r74
TitleStructure of the periplasmic binding protein AfuA from Actinobacillus pleuropneumoniae (exogenous fructose-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


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
6-O-phosphono-beta-D-fructofuranose / ABC-type Fe3+ transport system, periplasmic component
Similarity search - Component
Biological speciesActinobacillus pleuropneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 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 1.2Jul 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.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
Revision 1.3Nov 27, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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


Theoretical massNumber of molelcules
Total (without water)144,70632
Polymers141,5684
Non-polymers3,13828
Water17,276959
1
A: ABC-type Fe3+ transport system, periplasmic component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0206
Polymers35,3921
Non-polymers6295
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)36,3199
Polymers35,3921
Non-polymers9278
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ABC-type Fe3+ transport system, periplasmic component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2979
Polymers35,3921
Non-polymers9058
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: ABC-type Fe3+ transport system, periplasmic component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0698
Polymers35,3921
Non-polymers6777
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.202, 96.988, 145.075
Angle α, β, γ (deg.)90.00, 95.93, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 8 molecules ABCD

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


Mass: 35391.980 Da / Num. of mol.: 4 / 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
#2: Sugar
ChemComp-F6P / 6-O-phosphono-beta-D-fructofuranose / FRUCTOSE-6-PHOSPHATE / 6-O-phosphono-beta-D-fructose / 6-O-phosphono-D-fructose / 6-O-phosphono-fructose


Type: D-saccharide, beta linking / Mass: 260.136 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
b-D-Fruf6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 983 molecules

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


Mass: 92.094 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 959 / 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: 2.14 Å3/Da / Density % sol: 42.4 %
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: APS / Beamline: 24-ID-E / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) side bounce
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.93→48.494 Å / Num. all: 89478 / Num. obs: 89478 / % possible obs: 100 % / Redundancy: 7.6 % / Biso Wilson estimate: 18.89 Å2 / Rsym value: 0.131 / Net I/σ(I): 14.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
1.93-2.037.50.8170.90.817199.9
2.03-2.167.60.5131.50.5131100
2.16-2.317.60.3432.20.3431100
2.31-2.497.60.2530.251100
2.49-2.737.60.1844.10.1841100
2.73-3.057.60.1216.30.1211100
3.05-3.527.60.07310.20.0731100
3.52-4.317.40.04715.30.0471100
4.31-6.17.40.03917.40.0391100
6.1-48.4947.50.03320.40.033199.9

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→48.494 Å / SU ML: 0.2 / σ(F): 1.34 / Phase error: 19.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2018 4485 5.01 %
Rwork0.1514 --
obs0.154 89444 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.9459 Å2
Refinement stepCycle: LAST / Resolution: 1.93→48.494 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9919 0 199 959 11077
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810447
X-RAY DIFFRACTIONf_angle_d1.12514121
X-RAY DIFFRACTIONf_dihedral_angle_d16.1843928
X-RAY DIFFRACTIONf_chiral_restr0.0451534
X-RAY DIFFRACTIONf_plane_restr0.0051793
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.95150.25571720.21582801X-RAY DIFFRACTION100
1.9515-1.97450.25531430.21812864X-RAY DIFFRACTION100
1.9745-1.99860.27651420.20532805X-RAY DIFFRACTION100
1.9986-2.02390.25661720.19742786X-RAY DIFFRACTION100
2.0239-2.05050.24981590.19122833X-RAY DIFFRACTION100
2.0505-2.07860.23551540.18382816X-RAY DIFFRACTION100
2.0786-2.10830.2461480.17772783X-RAY DIFFRACTION100
2.1083-2.13980.24741470.17152817X-RAY DIFFRACTION100
2.1398-2.17320.25641410.17152874X-RAY DIFFRACTION100
2.1732-2.20880.22611370.17252811X-RAY DIFFRACTION100
2.2088-2.24690.22451200.16372837X-RAY DIFFRACTION100
2.2469-2.28780.22661400.1642873X-RAY DIFFRACTION100
2.2878-2.33180.23151550.16062771X-RAY DIFFRACTION100
2.3318-2.37940.2261600.16212830X-RAY DIFFRACTION100
2.3794-2.43110.21661350.1592836X-RAY DIFFRACTION100
2.4311-2.48760.19851480.15752820X-RAY DIFFRACTION100
2.4876-2.54990.22431360.15712879X-RAY DIFFRACTION100
2.5499-2.61880.21231350.15112791X-RAY DIFFRACTION100
2.6188-2.69580.22821510.15082861X-RAY DIFFRACTION100
2.6958-2.78290.19431310.15022828X-RAY DIFFRACTION100
2.7829-2.88230.22591550.15182870X-RAY DIFFRACTION100
2.8823-2.99770.2241300.15032797X-RAY DIFFRACTION100
2.9977-3.13410.20011570.15022842X-RAY DIFFRACTION100
3.1341-3.29930.19311600.14422839X-RAY DIFFRACTION100
3.2993-3.5060.17531590.13772802X-RAY DIFFRACTION100
3.506-3.77660.17731610.1262829X-RAY DIFFRACTION100
3.7766-4.15640.16571520.11712848X-RAY DIFFRACTION100
4.1564-4.75740.14281530.12382880X-RAY DIFFRACTION100
4.7574-5.99210.17251820.13832808X-RAY DIFFRACTION100
5.9921-48.50930.17041500.14542928X-RAY DIFFRACTION100

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