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- PDB-2r6g: The Crystal Structure of the E. coli Maltose Transporter -

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Basic information

Entry
Database: PDB / ID: 2r6g
TitleThe Crystal Structure of the E. coli Maltose Transporter
Components
  • (Maltose transport system permease protein ...) x 2
  • Maltose-binding periplasmic protein
  • Maltose/maltodextrin import ATP-binding protein malK
KeywordsHYDROLASE/TRANSPORT PROTEIN / ABC transporter / catalytic intermediate / E. coli maltose transporter / MBP / maltodextrin binding protein / MalK / ATP binding cassette / ATP-binding / Hydrolase / Inner membrane / Membrane / Nucleotide-binding / Sugar transport / Transmembrane / HYDROLASE-TRANSPORT PROTEIN COMPLEX
Function / homology
Function and homology information


ABC-type maltose transporter / ABC-type maltose transporter activity / negative regulation of maltose transport / enzyme IIA-maltose transporter complex / negative regulation of transmembrane transport / detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport ...ABC-type maltose transporter / ABC-type maltose transporter activity / negative regulation of maltose transport / enzyme IIA-maltose transporter complex / negative regulation of transmembrane transport / 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 / DNA-binding transcription factor binding / periplasmic space / DNA damage response / ATP hydrolysis activity / ATP binding / membrane / plasma membrane
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 / Maltose transport system permease protein MalF, P2 domain / MalF, N-terminal / : / : / 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 / 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 / MalK, OB fold domain / MalK OB fold domain / ABC transporter, maltose/maltodextrin import, MalK-like / : / Molybdate/tungstate binding, C-terminal / 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 / 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 / Nucleic acid-binding proteins / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / ABC transporter-like, conserved site / ABC transporters family signature. / Periplasmic binding protein-like II / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / D-Maltodextrin-Binding Protein; domain 2 / 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
alpha-maltose / ADENOSINE-5'-TRIPHOSPHATE / Maltose/maltodextrin transport system permease protein MalF / Maltose/maltodextrin-binding periplasmic protein / Maltose/maltodextrin transport system permease protein MalG / Maltose/maltodextrin import ATP-binding protein MalK / Maltose/maltodextrin import ATP-binding protein MalK
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsOldham, M.L. / Khare, D. / Quiocho, F.A. / Davidson, A.L. / Chen, J.
CitationJournal: Nature / Year: 2007
Title: Crystal structure of a catalytic intermediate of the maltose transporter.
Authors: Oldham, M.L. / Khare, D. / Quiocho, F.A. / Davidson, A.L. / Chen, J.
History
DepositionSep 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _struct_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
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
Revision 2.2Aug 30, 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

Downloads & links

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Assembly

Deposited unit
A: Maltose/maltodextrin import ATP-binding protein malK
B: Maltose/maltodextrin import ATP-binding protein malK
E: Maltose-binding periplasmic protein
F: Maltose transport system permease protein malF
G: Maltose transport system permease protein malG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,7768
Polymers214,4195
Non-polymers1,3573
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.260, 95.860, 109.990
Angle α, β, γ (deg.)87.13, 82.43, 75.75
Int Tables number1
Space group name H-MP1

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Components

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Protein , 2 types, 3 molecules ABE

#1: Protein Maltose/maltodextrin import ATP-binding protein malK


Mass: 42183.551 Da / Num. of mol.: 2 / Mutation: E159Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: malK / Production host: Escherichia coli (E. coli) / Strain (production host): HN741
References: UniProt: Q1R3Q1, UniProt: P68187*PLUS, EC: 3.6.3.19
#2: Protein Maltose-binding periplasmic protein / Maltodextrin-binding protein / MBP


Mass: 40753.152 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: malE / Production host: Escherichia coli (E. coli) / Strain (production host): BAR1000 / References: UniProt: P0AEX9

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Maltose transport system permease protein ... , 2 types, 2 molecules FG

#3: Protein Maltose transport system permease protein malF


Mass: 57052.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: malF / Production host: Escherichia coli (E. coli) / Strain (production host): HN741 / References: UniProt: P02916
#4: Protein Maltose transport system permease protein malG


Mass: 32246.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: malG / Production host: Escherichia coli (E. coli) / Strain (production host): HN741 / References: UniProt: P68183

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Sugars / Non-polymers , 2 types, 3 molecules

#5: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#6: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*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: 3.46 Å3/Da / Density % sol: 64.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 27% PEG 400, 500mM NaCl, 100mM Sodium Hepes pH 7.5, 10mM betaine hydrochloride, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 30, 2007
Details: Si(111) Double Crystal Monochromator. Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionRedundancy: 3.6 % / Av σ(I) over netI: 8.3 / Number: 236250 / Rmerge(I) obs: 0.092 / Χ2: 1.09 / D res high: 2.8 Å / D res low: 50 Å / Num. obs: 66520 / % possible obs: 91.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.035099.110.0431.0423.9
4.796.0399.510.071.0234
4.184.7999.310.0791.0724
3.84.189910.1171.1353.9
3.533.89910.1621.123.8
3.323.5398.710.241.13.6
3.153.3295.410.3431.1353.3
3.023.1585.910.4061.1153
2.93.0273.510.4691.0982.8
2.82.964.910.471.0412.6
ReflectionResolution: 2.8→50 Å / Num. all: 66520 / Num. obs: 66520 / % possible obs: 91.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 8.3
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.54 / Rsym value: 0.47 / % possible all: 64.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4 Å14.98 Å
Translation4 Å14.98 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 60264
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
13.97-10063.40.632509
10.21-13.97530.893889
8.43-10.2147.80.921137
7.35-8.4347.50.8991311
6.59-7.3546.60.8911489
6.03-6.5947.30.8941625
5.6-6.0347.30.8951771
5.24-5.646.70.9091896
4.95-5.2444.70.9121997
4.7-4.9545.70.9292132
4.48-4.746.40.9362202
4.29-4.4846.10.9312284
4.13-4.2945.70.9282371
3.98-4.1347.60.9212449
3.84-3.98490.9282486
3.72-3.8448.10.9322587
3.61-3.7248.90.9322628
3.51-3.6152.20.9212642
3.42-3.5151.20.9152687
3.33-3.4252.20.9182691
3.25-3.33520.92757
3.18-3.2553.40.9012610
3.11-3.1853.90.8912640
3.04-3.1153.70.8962453
2.98-3.0452.60.8852267
2.93-2.9853.80.8812120
2.87-2.9353.40.8752063
2.82-2.8756.20.851855
2.76-2.8255.20.8111716

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
DM6phasing
REFMACrefinement
PDB_EXTRACT3data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1Q12 and 1OMP

1q12

1omp


Resolution: 2.8→47.4 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.899 / SU B: 40.785 / SU ML: 0.361 / Cross valid method: THROUGHOUT / ESU R Free: 0.408 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2714 1185 2 %RANDOM
Rwork0.24164 ---
obs0.24223 58103 83.76 %-
all-59288 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 83.877 Å2
Baniso -1Baniso -2Baniso -3
1-3.95 Å23.16 Å25.32 Å2
2---2.54 Å2-2.06 Å2
3----4.16 Å2
Refinement stepCycle: LAST / Resolution: 2.8→47.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14628 0 85 0 14713
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02215045
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9741.97520472
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.46851880
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.75824.226620
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.378152500
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1721577
X-RAY DIFFRACTIONr_chiral_restr0.0640.22353
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0211236
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1760.27470
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2960.210425
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1070.2480
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.249
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0750.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1431.59633
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.257215112
X-RAY DIFFRACTIONr_scbond_it0.22836172
X-RAY DIFFRACTIONr_scangle_it0.3864.55360
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 50 -
Rwork0.33 2595 -
obs--50.88 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.99621.2838-0.29761.06610.22710.7725-0.20780.03630.41930.098-0.13090.14140.6217-0.4160.33880.45620.07720.01410.38150.09740.4217-19.1057-10.754916.9514
20.74570.018-0.03882.60381.12151.7660.047-0.0461-0.0949-0.13390.018-0.23250.19590.1322-0.0650.2530.02520.01240.19770.06910.311-5.3096-6.57314.1614
32.41130.1754-0.57091.9850.40281.76760.0650.1310.0613-0.49570.0388-0.3526-0.30490.1072-0.10380.4077-0.00890.10370.12540.07460.2167-1.419916.5103-1.7983
43.55252.2461-0.19514.2545-0.9082.2540.08620.0665-0.3202-0.32120.0182-1.56280.04720.7272-0.10440.37460.05710.30170.3488-0.10010.68320.9404-2.4292-3.8597
50.9323-0.3410.04361.1543-0.54362.55760.15670.15950.139-0.0124-0.02710.0828-0.5914-0.5183-0.12960.36390.14360.04260.18790.02740.2008-46.736762.938257.4496
60.0090.0269-0.02650.0803-0.07910.07790.1708-1.0568-0.66551.20040.3481-0.13930.91480.8805-0.51890.6082-0.00370.00030.60290.00090.6091-30.508411.642761.1635
70.3068-0.2984-0.62751.0670.95592.3398-0.16460.1153-0.13770.4212-0.16280.30680.4401-0.46310.32740.4149-0.12750.08130.203-0.02060.3001-50.003438.15678.234
80.516-0.3936-0.95251.22470.49742.55260.18790.22190.0234-0.291-0.19880.0963-0.1684-0.54370.0110.18410.0396-0.05690.30630.02520.1857-35.148341.389327.7415
91.7327-0.66990.30523.9694-1.57050.9065-0.25620.1873-0.0907-0.5825-0.11760.00350.0543-0.58160.37390.1028-0.0726-0.05790.5366-0.08150.2143-51.095541.4438.5284
100.8512-0.6095-0.76872.35971.09772.54130.09530.15130.0623-0.0867-0.06930.0398-0.1099-0.0862-0.02590.137-0.048-0.04920.2770.07490.3593-24.803842.701339.4226
110.8492-0.9237-0.72611.8321.36722.150.0148-0.05880.03540.1533-0.0453-0.05480.2117-0.01670.03050.2539-0.0509-0.04240.26860.06510.3155-22.127131.803541.7299
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 292 - 29
2X-RAY DIFFRACTION2AA30 - 37230 - 372
3X-RAY DIFFRACTION3BB2 - 2672 - 267
4X-RAY DIFFRACTION4BB268 - 373268 - 373
5X-RAY DIFFRACTION5EC1 - 3701 - 370
6X-RAY DIFFRACTION6FD13 - 5313 - 53
7X-RAY DIFFRACTION7FD54 - 24854 - 248
8X-RAY DIFFRACTION8FD249 - 441249 - 441
9X-RAY DIFFRACTION9FD442 - 504442 - 504
10X-RAY DIFFRACTION10GE7 - 1457 - 145
11X-RAY DIFFRACTION11GE146 - 296146 - 296

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