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- PDB-3kjt: Stimulation of the maltose transporter by a mutant sucrose bindin... -

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Basic information

Entry
Database: PDB / ID: 3kjt
TitleStimulation of the maltose transporter by a mutant sucrose binding protein gives insights into ABC transporter coupling
ComponentsMaltose-binding periplasmic protein
KeywordsTRANSPORT PROTEIN / Alternate conformation / Periplasm / Sugar transport / Transport
Function / homology
Function and homology information


detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / 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
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsGould, A.D. / Shilton, B.H.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Studies of the maltose transport system reveal a mechanism for coupling ATP hydrolysis to substrate translocation without direct recognition of substrate.
Authors: Gould, A.D. / Shilton, B.H.
History
DepositionNov 3, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 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 1.3Sep 6, 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)40,9081
Polymers40,9081
Non-polymers00
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.89, 65.54, 57.50
Angle α, β, γ (deg.)90.00, 101.14, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 40908.371 Da / Num. of mol.: 1 / Fragment: UNP residues 27-396 / Mutation: D14L, K15F, W62Y, E111Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: b4034, JW3994, malE / Plasmid: pPROEX-hta / Production host: Escherichia coli (E. coli) / Strain (production host): HS3309 / References: UniProt: P0AEX9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 1.98 Å3/Da / Density % sol: 37.99 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG MME 5000, 0.1M Sodium acetate, 60mM MgCl2, 10mM ZnCl2, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 13, 2009 / Details: ACCEL DCM and vertically focusing mirror
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.5→24.8 Å / Num. obs: 48552 / % possible obs: 85.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 17.79
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.329 / Mean I/σ(I) obs: 2.03 / Num. unique all: 4212 / % possible all: 82.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1OMP

1omp


Resolution: 1.5→24.8 Å / Occupancy max: 1 / Occupancy min: 0 / Cross valid method: THROUGHOUT / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.242 2346 4.7 %Random
Rwork0.213 ---
all0.221 48552 --
obs0.215 48233 85.2 %-
Solvent computationBsol: 54.674 Å2
Displacement parametersBiso max: 59.58 Å2 / Biso mean: 16.158 Å2 / Biso min: 5.89 Å2
Baniso -1Baniso -2Baniso -3
1-0.239 Å20 Å2-0.943 Å2
2--0.931 Å20 Å2
3----1.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.08 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.5→24.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2881 0 0 220 3101
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.166
X-RAY DIFFRACTIONc_mcbond_it1.1941.5
X-RAY DIFFRACTIONc_scbond_it2.3942
X-RAY DIFFRACTIONc_mcangle_it1.7792
X-RAY DIFFRACTIONc_scangle_it3.5152.5
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.015
RfactorNum. reflection% reflection
Rfree0.268 324 -
Rwork0.262 --
obs-6847 84.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top

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