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- PDB-1peb: LIGAND-FREE HIGH-AFFINITY MALTOSE-BINDING PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1peb
TitleLIGAND-FREE HIGH-AFFINITY MALTOSE-BINDING PROTEIN
ComponentsMaltose-binding periplasmic protein
KeywordsSUGAR BINDING PROTEIN / MBP / MALTOSE-BINDING PROTEIN / HIGH-AFFINITY MUTANT / ENGINEERED
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
Maltose/maltodextrin-binding periplasmic protein / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsTelmer, P.G. / Shilton, B.H.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Insights into the Conformational Equilibria of Maltose-binding Protein by Analysis of High Affinity Mutants.
Authors: Telmer, P.G. / Shilton, B.H.
History
DepositionMay 21, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maltose-binding periplasmic protein


Theoretical massNumber of molelcules
Total (without water)40,1001
Polymers40,1001
Non-polymers00
Water1,63991
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.540, 70.350, 58.190
Angle α, β, γ (deg.)90.00, 101.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 40100.422 Da / Num. of mol.: 1 / Mutation: M321A, Q325A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: MALE OR B4034 OR Z5632 OR ECS5017 / Plasmid: pLH1 / Production host: Escherichia coli (E. coli) / Strain (production host): HS3309 / References: UniProt: P02928, UniProt: P0AEX9*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 312 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 3500, cacodylic acid, zinc acetate, sodium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 312K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54179 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 2003
RadiationMonochromator: GRADED MULTILAYER (OSMIC) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.6→100 Å / Num. all: 10584 / Num. obs: 10346 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 29.4 Å2 / Rmerge(I) obs: 0.053
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.181 / % possible all: 95.3
Reflection shell
*PLUS
% possible obs: 95.3 %

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1MPB

1mpb


Resolution: 2.6→16.88 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: RESOLUTION-DEPENDENT WEIGHTING SCHEME, BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1051 10.3 %RANDOM
Rwork0.181 ---
obs0.181 10198 93.6 %-
all-10198 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.1629 Å2 / ksol: 0.309377 e/Å3
Displacement parametersBiso mean: 34.2 Å2
Baniso -1Baniso -2Baniso -3
1--5.42 Å20 Å2-3.49 Å2
2--6.38 Å20 Å2
3----0.96 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.6→16.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2833 0 0 91 2924
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_mcbond_it1.91.5
X-RAY DIFFRACTIONc_mcangle_it2.72
X-RAY DIFFRACTIONc_scbond_it1.972
X-RAY DIFFRACTIONc_scangle_it3.092.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.341 158 9 %
Rwork0.229 1603 -
obs-1603 96.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION4CARBOHYDRATE.PARAMION.TOP
X-RAY DIFFRACTION5MALTOSE.PARA
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 16.9 Å
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
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.9

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