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- PDB-1lls: CRYSTAL STRUCTURE OF UNLIGANDED MALTOSE BINDING PROTEIN WITH XENON -

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Basic information

Entry
Database: PDB / ID: 1lls
TitleCRYSTAL STRUCTURE OF UNLIGANDED MALTOSE BINDING PROTEIN WITH XENON
ComponentsMaltose-binding periplasmic protein
KeywordsSUGAR BINDING PROTEIN / Hydrophobic Cavities / Ligand-Protein Interactions / Xenon Binding / Xenon Derivative
Function / homology
Function and homology information


detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / membrane
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 / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
XENON / Maltose/maltodextrin-binding periplasmic protein / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Isomorphous with Structure in Database / Resolution: 1.8 Å
AuthorsRubin, S.M. / Lee, S.-Y. / Ruiz, E.J. / Pines, A. / Wemmer, D.E.
Citation
Journal: J.MOL.BIOL. / Year: 2002
Title: DETECTION AND CHARACTERIZATION OF XENON-BINDING SITES IN PROTEINS BY 129XE NMR SPECTROSCOPY
Authors: Rubin, S.M. / Lee, S.-Y. / Ruiz, E.J. / Pines, A. / Wemmer, D.E.
#1: Journal: J.Am.Chem.Soc. / Year: 2001
Title: Detection of a Conformational Change in Maltose Binding Protein by 129Xe Nuclear Magnetic Resonance
Authors: Rubin, S.M. / Spence, M.M. / Dimitrov, I.E. / Ruiz, E.J. / Pines, A. / Wemmer, D.E.
#2: Journal: J.Biol.Chem. / Year: 1991
Title: The 2.3 A Structure of the Malto- or Maltodextrin-Binding Protein, a Primary Receptor of Bacterial Active Transport
Authors: Spurlino, J.C. / Lu, G.-Y. / Quiocho, F.A.
#3: Journal: Biochemistry / Year: 1992
Title: Crystallographic Evidence of a Large Ligand-Induced Hinge-Twist Motion Between the Two Domains of the Maltodextrin Binding Protein Involved in Active Transport and Chemotaxis
Authors: Sharff, A.J. / Rodseth, L.E. / Spurlino, J.C. / Quiocho, F.A.
#4: Journal: J.Mol.Biol. / Year: 2000
Title: Size Versus Polarizability in Protein-Ligand Interactions: Binding of Noble Gases within Engineered Cavities in Phage T4 Lysozyme
Authors: Quillin, M.L. / Breyer, W.A. / Griswold, I.J. / Matthews, B.W.
History
DepositionApr 30, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Maltose-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8842
Polymers40,7531
Non-polymers1311
Water3,081171
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.207, 44.026, 57.649
Angle α, β, γ (deg.)100.75, 101.36, 102.62
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 40753.152 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P02928, UniProt: P0AEX9*PLUS
#2: Chemical ChemComp-XE / XENON


Mass: 131.293 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Xe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.21 Å3/Da / Density % sol: 44.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 10 mM Sodium Citrate, 23% PEG 8000, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
116 mg/mlprotein1drop
210 mMsodium citrate1reservoir
323 %(w/v)PEG80001reservoirpH6.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC / Detector: CCD / Date: Jan 31, 2002
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→17.07 Å / Num. all: 55908 / Num. obs: 29855 / % possible obs: 92.3 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 4 / Biso Wilson estimate: 16.9 Å2 / Rsym value: 0.029 / Net I/σ(I): 19.9
Reflection shellResolution: 1.8→1.91 Å / Mean I/σ(I) obs: 10.4 / Num. unique all: 4127 / Rsym value: 0.105 / % possible all: 76
Reflection
*PLUS
Num. measured all: 55908 / Rmerge(I) obs: 0.029

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Processing

Software
NameVersionClassification
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: Isomorphous with Structure in Database
Starting model: PDB ENTRY 1OMP

1omp


Resolution: 1.8→17.07 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1472 4.9 %RANDOM
Rwork0.204 ---
all0.2051 29855 --
obs0.204 29855 92.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.8917 Å2 / ksol: 0.387004 e/Å3
Displacement parametersBiso mean: 22.5 Å2
Baniso -1Baniso -2Baniso -3
1-8.82 Å24.28 Å20.45 Å2
2---4.1 Å2-0.33 Å2
3----4.72 Å2
Refine analyzeLuzzati coordinate error free: 0.24 Å / Luzzati sigma a free: 0.15 Å
Refinement stepCycle: LAST / Resolution: 1.8→17.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2878 0 1 171 3050
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d0.91
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.258 207 5 %
Rwork0.241 3920 -
obs--76 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAM
X-RAY DIFFRACTION3WATER.PARAM
Refinement
*PLUS
Num. reflection obs: 29755 / Rfactor all: 0.2051 / Rfactor obs: 0.204 / Rfactor Rfree: 0.226 / Rfactor Rwork: 0.204
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.91
LS refinement shell
*PLUS
Rfactor Rfree: 0.258 / Rfactor Rwork: 0.241

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