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- PDB-2xd2: The crystal structure of MalX from Streptococcus pneumoniae -

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Basic information

Entry
Database: PDB / ID: 2xd2
TitleThe crystal structure of MalX from Streptococcus pneumoniae
ComponentsMALTOSE/MALTODEXTRIN-BINDING PROTEIN
KeywordsSUGAR BINDING PROTEIN / SOLUTE-BINDING PROTEIN / VIRULENCE / ALPHA-GLUCAN / SUGAR TRANSPORT / MEMBRANE PROTEIN
Function / homology
Function and homology information


maltoheptaose binding / maltodextrin transmembrane transporter activity / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / plasma membrane
Similarity search - Function
Bacterial extracellular solute-binding protein / 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 / 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
Maltooligosaccharide ABC transporter solute-binding lipoprotein
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsAbbott, D.W. / Higgins, M.A. / Hyrnuik, S. / Pluvinage, B. / Lammerts van Bueren, A. / Boraston, A.B.
CitationJournal: Mol.Microbiol. / Year: 2010
Title: The Molecular Basis of Glycogen Breakdown and Transport in Streptococcus Pneumoniae.
Authors: Abbott, D.W. / Higgins, M.A. / Hyrnuik, S. / Pluvinage, B. / Lammerts Van Bueren, A. / Boraston, A.B.
History
DepositionApr 28, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MALTOSE/MALTODEXTRIN-BINDING PROTEIN
B: MALTOSE/MALTODEXTRIN-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)89,8562
Polymers89,8562
Non-polymers00
Water1,04558
1
A: MALTOSE/MALTODEXTRIN-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)44,9281
Polymers44,9281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: MALTOSE/MALTODEXTRIN-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)44,9281
Polymers44,9281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)181.305, 56.940, 113.690
Angle α, β, γ (deg.)90.00, 128.83, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein MALTOSE/MALTODEXTRIN-BINDING PROTEIN / MALX


Mass: 44928.016 Da / Num. of mol.: 2 / Fragment: RESIDUES 31-423
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: TIGR4 / Plasmid: PMALX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P59213
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.54 Å3/Da / Density % sol: 51.65 % / Description: NONE

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. obs: 85794 / % possible obs: 96.4 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.9
Reflection shellResolution: 2.9→2.97 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.4 / % possible all: 95.4

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→20 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.868 / SU B: 17.947 / SU ML: 0.346 / Cross valid method: THROUGHOUT / ESU R Free: 0.456 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27392 998 5.1 %RANDOM
Rwork0.21578 ---
obs0.21885 18625 96.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.028 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20 Å2-3.26 Å2
2---0.98 Å20 Å2
3----2.54 Å2
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5740 0 0 58 5798
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0225850
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0621.9587930
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1585752
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.28226.772254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.0415988
X-RAY DIFFRACTIONr_dihedral_angle_4_deg31.749154
X-RAY DIFFRACTIONr_chiral_restr0.0760.2876
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214428
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.3731.53726
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.69725938
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.70932124
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.264.51992
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.974 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 86 -
Rwork0.292 1351 -
obs--95.36 %

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