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- PDB-4jbw: Crystal structure of E. coli maltose transporter MalFGK2 in compl... -

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Basic information

Entry
Database: PDB / ID: 4jbw
TitleCrystal structure of E. coli maltose transporter MalFGK2 in complex with its regulatory protein EIIAglc
Components
  • Glucose-specific phosphotransferase enzyme IIA component
  • Maltose transport system permease protein MalF
  • Maltose transport system permease protein MalG
  • Maltose/maltodextrin import ATP-binding protein MalK
KeywordsTRANSPORT PROTEIN / ABC transporter ATPase inducer exclusion carbon catabolite repression
Function / homology
Function and homology information


negative regulation of carbohydrate metabolic process / ABC-type maltose transporter / ABC-type maltose transporter activity / negative regulation of maltose transport / enzyme IIA-maltose transporter complex / negative regulation of transmembrane transport / phosphoenolpyruvate-dependent sugar phosphotransferase system / transmembrane transporter complex / maltose transport complex / maltose transport ...negative regulation of carbohydrate metabolic process / ABC-type maltose transporter / ABC-type maltose transporter activity / negative regulation of maltose transport / enzyme IIA-maltose transporter complex / negative regulation of transmembrane transport / phosphoenolpyruvate-dependent sugar phosphotransferase system / transmembrane transporter complex / maltose transport complex / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / kinase activity / DNA-binding transcription factor binding / phosphorylation / DNA damage response / ATP hydrolysis activity / ATP binding / membrane / metal ion binding / plasma membrane / cytosol
Similarity search - Function
MalF N-terminal region-like / Periplasmic binding protein-like II / D-maltodextrin-binding protein, MBP / MalF N-terminal region-like / MalF N-terminal region-like / PTS EIIA domains phosphorylation site signature 1. / Phosphotransferase system, sugar-specific permease EIIA type 1 / phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 1 / PTS_EIIA type-1 domain profile. / Maltose transport system permease protein MalF, P2 domain ...MalF N-terminal region-like / Periplasmic binding protein-like II / D-maltodextrin-binding protein, MBP / MalF N-terminal region-like / MalF N-terminal region-like / PTS EIIA domains phosphorylation site signature 1. / Phosphotransferase system, sugar-specific permease EIIA type 1 / phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 1 / PTS_EIIA type-1 domain profile. / Maltose transport system permease protein MalF, P2 domain / MalF, N-terminal / : / : / Maltose transport system permease protein MalF P2 domain / MalF, N-terminal region, transmembrane helices / MetI-like fold / MetI-like / Maltose/Maltodextrin import ATP-binding protein malK family profile. / Transport-associated OB, type 2 / TOBE domain / Glucose Permease (Domain IIA) / Glucose Permease (Domain IIA) / MalK OB fold domain / ABC transporter, maltose/maltodextrin import, MalK-like / : / Molybdate/tungstate binding, C-terminal / Duplicated hybrid motif / ABC transporter type 1, transmembrane domain MetI-like / MetI-like superfamily / Binding-protein-dependent transport system inner membrane component / ABC transporter integral membrane type-1 domain profile. / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Nucleic acid-binding proteins / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / Distorted Sandwich / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Nucleic acid-binding, OB-fold / Roll / Up-down Bundle / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-PGV / Maltose/maltodextrin transport system permease protein MalF / Maltose/maltodextrin transport system permease protein MalG / Maltose/maltodextrin import ATP-binding protein MalK / PTS system glucose-specific EIIA component
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.913 Å
AuthorsChen, S. / Oldham, M.L. / Davidson, A.L. / Chen, J.
CitationJournal: Nature / Year: 2013
Title: Carbon catabolite repression of the maltose transporter revealed by X-ray crystallography.
Authors: Chen, S. / Oldham, M.L. / Davidson, A.L. / Chen, J.
History
DepositionFeb 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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
F: Maltose transport system permease protein MalF
G: Maltose transport system permease protein MalG
A: Maltose/maltodextrin import ATP-binding protein MalK
B: Maltose/maltodextrin import ATP-binding protein MalK
M: Glucose-specific phosphotransferase enzyme IIA component
N: Glucose-specific phosphotransferase enzyme IIA component
H: Maltose transport system permease protein MalF
I: Maltose transport system permease protein MalG
C: Maltose/maltodextrin import ATP-binding protein MalK
D: Maltose/maltodextrin import ATP-binding protein MalK
O: Glucose-specific phosphotransferase enzyme IIA component
P: Glucose-specific phosphotransferase enzyme IIA component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)423,01614
Polymers421,51812
Non-polymers1,4982
Water0
1
F: Maltose transport system permease protein MalF
G: Maltose transport system permease protein MalG
A: Maltose/maltodextrin import ATP-binding protein MalK
B: Maltose/maltodextrin import ATP-binding protein MalK
M: Glucose-specific phosphotransferase enzyme IIA component
N: Glucose-specific phosphotransferase enzyme IIA component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,5087
Polymers210,7596
Non-polymers7491
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
H: Maltose transport system permease protein MalF
I: Maltose transport system permease protein MalG
C: Maltose/maltodextrin import ATP-binding protein MalK
D: Maltose/maltodextrin import ATP-binding protein MalK
O: Glucose-specific phosphotransferase enzyme IIA component
P: Glucose-specific phosphotransferase enzyme IIA component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,5087
Polymers210,7596
Non-polymers7491
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.529, 208.448, 347.477
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsBiological unit: chains H,I,C,D,O, and P (2nd equivalent NCS mate)

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Components

#1: Protein Maltose transport system permease protein MalF


Mass: 57052.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: malF, b4033, JW3993 / Production host: Escherichia coli (E. coli) / References: UniProt: P02916
#2: Protein Maltose transport system permease protein MalG


Mass: 32246.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: malG, b4032, JW3992 / Production host: Escherichia coli (E. coli) / References: UniProt: P68183
#3: Protein
Maltose/maltodextrin import ATP-binding protein MalK


Mass: 42184.535 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: malK, b4035, JW3995 / Production host: Escherichia coli (E. coli) / References: UniProt: P68187, EC: 3.6.3.19
#4: Protein
Glucose-specific phosphotransferase enzyme IIA component / EIIA-Glc / EIII-Glc / PTS system glucose-specific EIIA component


Mass: 18545.289 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: crr, gsr, iex, tgs, treD, b2417, JW2410 / Production host: Escherichia coli (E. coli)
References: UniProt: P69783, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#5: Chemical ChemComp-PGV / (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE / PHOSPHATIDYLGLYCEROL / 2-VACCENOYL-1-PALMITOYL-SN-GLYCEROL-3-PHOSPHOGLYCEROL / Phosphatidylglycerol


Mass: 749.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H77O10P / Comment: phospholipid*YM

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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: 4.06 Å3/Da / Density % sol: 69.71 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 13% PEG monomethylether 2000, 100mM Sodium cacodylate pH 5.6, 100mM Non Detergent Sulfobetaine (NDSB-256), VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 12, 2012
RadiationMonochromator: double crystal monochromator and vertically focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.913→20 Å / Num. all: 59277 / Num. obs: 59277 / % possible obs: 95 % / Redundancy: 4.9 % / Rsym value: 0.106 / Net I/σ(I): 13.8
Reflection shellResolution: 3.913→4.06 Å / % possible all: 96.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F3G, 3FH6, and 3PV0

1f3g

3fh6

3pv0


Resolution: 3.913→19.975 Å / SU ML: 0.6 / σ(F): 1.33 / Phase error: 31.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2812 3015 5.09 %
Rwork0.226 --
obs0.2288 59228 94.86 %
all-59277 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.913→19.975 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27906 0 52 0 27958
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00228522
X-RAY DIFFRACTIONf_angle_d0.64638756
X-RAY DIFFRACTIONf_dihedral_angle_d12.4710432
X-RAY DIFFRACTIONf_chiral_restr0.0394553
X-RAY DIFFRACTIONf_plane_restr0.0034945
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.9126-3.97330.37271150.32782443X-RAY DIFFRACTION92
3.9733-4.03790.3651340.33132565X-RAY DIFFRACTION97
4.0379-4.10690.37221360.32282611X-RAY DIFFRACTION97
4.1069-4.1810.41571340.33452518X-RAY DIFFRACTION96
4.181-4.26060.34891310.30842584X-RAY DIFFRACTION96
4.2606-4.34670.38461460.29442569X-RAY DIFFRACTION96
4.3467-4.44020.3281450.28482536X-RAY DIFFRACTION97
4.4402-4.54230.39411610.26782574X-RAY DIFFRACTION96
4.5423-4.65450.31791400.25242566X-RAY DIFFRACTION96
4.6545-4.77870.2851170.23172595X-RAY DIFFRACTION96
4.7787-4.91730.29381400.22632542X-RAY DIFFRACTION96
4.9173-5.07350.28361310.21552585X-RAY DIFFRACTION96
5.0735-5.25170.29261240.22072601X-RAY DIFFRACTION96
5.2517-5.45780.30511370.21412542X-RAY DIFFRACTION95
5.4578-5.70070.28191300.21372564X-RAY DIFFRACTION95
5.7007-5.99360.27471720.20352550X-RAY DIFFRACTION95
5.9936-6.35770.27231540.21022548X-RAY DIFFRACTION95
6.3577-6.83030.28691220.20592552X-RAY DIFFRACTION94
6.8303-7.48460.28431360.21372550X-RAY DIFFRACTION93
7.4846-8.49390.20391280.19172565X-RAY DIFFRACTION93
8.4939-10.44070.23791460.16972529X-RAY DIFFRACTION91
10.4407-19.97570.24691360.22552524X-RAY DIFFRACTION89

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