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- PDB-8c8f: Crystal structure of the E. coli maltodextrin-binding protein -

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Basic information

Entry
Database: PDB / ID: 8c8f
TitleCrystal structure of the E. coli maltodextrin-binding protein
ComponentsMaltose/maltodextrin-binding periplasmic protein
KeywordsSUGAR BINDING PROTEIN / Maltose Binding Protein / Native MBP
Function / homology
Function and homology information


carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / outer membrane-bounded periplasmic space
Similarity search - Function
Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsMarquez Espinoza, A. / Rodrigues, M.J. / Olieric, V. / Freisinger, E.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: To Be Published
Title: Crystal structure of the E. coli maltodextrin-binding protein
Authors: Marquez Espinoza, A. / Rodrigues, M.J. / Olieric, V. / Freisinger, E.
History
DepositionJan 19, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltose/maltodextrin-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5432
Polymers43,4361
Non-polymers1061
Water7,062392
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint2 kcal/mol
Surface area15640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.709, 64.961, 57.090
Angle α, β, γ (deg.)90.00, 101.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Maltose/maltodextrin-binding periplasmic protein / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP


Mass: 43436.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21 (bacteria) / References: UniProt: P0AEY0
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.95 Å3/Da / Density % sol: 36.99 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris pH 7.4, 30 % PEG Smear Broad, 0.1 M NaBr and 0.1 M KSCN

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.15→56.04 Å / Num. obs: 110383 / % possible obs: 99.5 % / Redundancy: 6.4 % / CC1/2: 0.999 / Net I/σ(I): 13.3
Reflection shellResolution: 1.15→1.17 Å / Num. unique obs: 5258 / CC1/2: 0.799

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.15→37.76 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.965 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.031 / ESU R Free: 0.032 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15203 5585 5.1 %RANDOM
Rwork0.12355 ---
obs0.12498 104767 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.422 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å2-0.12 Å2
2--0.12 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.15→37.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2853 0 7 392 3252
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0133044
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172830
X-RAY DIFFRACTIONr_angle_refined_deg1.9831.6454144
X-RAY DIFFRACTIONr_angle_other_deg1.671.5826604
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7935391
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.47124.964137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.62415515
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.811157
X-RAY DIFFRACTIONr_chiral_restr0.1290.2397
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023460
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02593
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9860.8641537
X-RAY DIFFRACTIONr_mcbond_other1.9840.8621536
X-RAY DIFFRACTIONr_mcangle_it2.5321.3061937
X-RAY DIFFRACTIONr_mcangle_other2.5331.3071938
X-RAY DIFFRACTIONr_scbond_it2.6081.1291507
X-RAY DIFFRACTIONr_scbond_other2.6171.131508
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0641.582208
X-RAY DIFFRACTIONr_long_range_B_refined3.24311.6443576
X-RAY DIFFRACTIONr_long_range_B_other3.08611.0983479
X-RAY DIFFRACTIONr_rigid_bond_restr3.5735874
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.15→1.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.192 406 -
Rwork0.163 7432 -
obs--95.38 %

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