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- PDB-4khz: Crystal structure of the maltose-binding protein/maltose transpor... -

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Basic information

Entry
Database: PDB / ID: 4khz
TitleCrystal structure of the maltose-binding protein/maltose transporter complex in an pre-translocation conformation bound to maltoheptaose
Components
  • (Binding-protein-dependent transport systems inner membrane ...) x 2
  • Maltose transport system permease protein MalF
  • Maltose-binding periplasmic protein
KeywordsTRANSPORT PROTEIN / ABC transporter / ATPase Maltodextrin transporter / ATP binding maltodextrin binding / inner membrane
Function / homology
Function and homology information


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 transport complex / maltose binding / maltose transport / maltodextrin transmembrane transport / carbohydrate transport ...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 transport complex / maltose binding / maltose transport / maltodextrin transmembrane transport / carbohydrate transport / carbohydrate transmembrane transporter activity / 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 / 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 / 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 / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / P-loop containing nucleotide triphosphate hydrolases / Roll / Up-down Bundle / Beta Barrel / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
alpha-maltotriose / alpha-maltotetraose / Chem-PGV / : / : / Maltose/maltodextrin transport system permease protein MalF / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsOldham, M.L. / Chen, S. / Chen, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structural basis for substrate specificity in the Escherichia coli maltose transport system.
Authors: Oldham, M.L. / Chen, S. / Chen, J.
History
DepositionMay 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2013Group: Database references
Revision 1.2Nov 27, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Maltose-binding periplasmic protein
F: Maltose transport system permease protein MalF
G: Binding-protein-dependent transport systems inner membrane component
A: Binding-protein-dependent transport systems inner membrane component
B: Binding-protein-dependent transport systems inner membrane component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,4878
Polymers215,5675
Non-polymers1,9203
Water95553
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.253, 92.221, 117.814
Angle α, β, γ (deg.)90.73, 101.68, 103.60
Int Tables number1
Space group name H-MP1
DetailsBiological assembly is composed of chains A,B,E,F, and G

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Components

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Protein , 2 types, 2 molecules EF

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


Mass: 41898.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b4034, JW3994, malE / Production host: Escherichia coli (E. coli) / Strain (production host): AD126 / References: UniProt: P0AEX9
#2: Protein Maltose transport system permease protein MalF


Mass: 57052.898 Da / Num. of mol.: 1 / Fragment: UNP residues 27-396
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b4033, JW3993, malF / Production host: Escherichia coli (E. coli) / Strain (production host): AD126 / References: UniProt: P02916

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Binding-protein-dependent transport systems inner membrane ... , 2 types, 3 molecules GAB

#3: Protein Binding-protein-dependent transport systems inner membrane component / Part of maltose permease / inner membrane component


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, DH1 / Gene: ECDH1ME8569_3888, EcDH1_3964, malG / Production host: Escherichia coli (E. coli) / Strain (production host): AD126 / References: UniProt: C9QV46
#4: Protein Binding-protein-dependent transport systems inner membrane component / Part of maltose permease / inner membrane component


Mass: 42184.535 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12, DH1 / Gene: ECDH1ME8569_3888, EcDH1_3964, malG, malK, O3O_01670 / Production host: Escherichia coli (E. coli) / Strain (production host): AD126 / References: UniProt: C9QV42

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Sugars , 2 types, 2 molecules

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


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotetraose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1a_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotriose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotriose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1a_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 2 types, 54 molecules

#7: 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.: 1 / Source method: obtained synthetically / Formula: C40H77O10P / Comment: phospholipid*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 3.65 Å3/Da / Density % sol: 66.31 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 30% poly-ethylene glycol 400, 100 mM NaCl, 10 mM MgCl2, 100 mM sodium HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.07216 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 15, 2011 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07216 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. all: 52859 / Num. obs: 52859 / % possible obs: 77.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.9→3 Å / % possible all: 30.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→19.81 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.871 / SU B: 42.703 / SU ML: 0.37 / Cross valid method: THROUGHOUT / ESU R Free: 0.527 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.283 2438 5 %RANDOM
Rwork0.24338 ---
obs0.24539 46052 71.65 %-
all-46052 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 97.709 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20.6 Å20.22 Å2
2---0.27 Å2-0.01 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 2.9→19.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14535 0 119 53 14707
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01914985
X-RAY DIFFRACTIONr_bond_other_d0.0010.0214682
X-RAY DIFFRACTIONr_angle_refined_deg0.7861.97720364
X-RAY DIFFRACTIONr_angle_other_deg0.656333703
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.48251868
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.18124.26622
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.595152495
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2971578
X-RAY DIFFRACTIONr_chiral_restr0.0450.22351
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02116783
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023349
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5995.1237490
X-RAY DIFFRACTIONr_mcbond_other0.5995.1237489
X-RAY DIFFRACTIONr_mcangle_it1.0637.6859352
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.4775.1867495
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.974 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 8 -
Rwork0.369 430 -
obs--8.93 %
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)
111.7072-0.2605-3.002610.65387.54266.79090.2245-1.04060.7310.6559-0.84670.8666-0.3714-0.83450.62220.9210.2563-0.26640.75740.02340.423-0.78790.54929.957
23.6211-1.5962-1.04936.20842.64717.3022-0.2160.3427-0.0685-0.9353-0.0183-0.104-1.1001-0.10590.23430.4427-0.1584-0.03110.14610.05160.199910.60879.27220.329
30.3296-0.7696-1.10293.76974.56718.4341-0.1651-0.0136-0.0455-0.1460.1634-0.3896-0.23710.57580.00170.2865-0.14580.07170.28290.05180.290814.39981.3637.503
410.21680.4373-1.525411.83334.17699.1426-0.0526-0.2335-0.0250.4409-0.2550.38610.1406-0.40510.30760.2622-0.07850.02950.3269-0.12180.16522.52796.42865.775
53.879-2.42912.53326.9435-0.97945.4002-0.2101-0.5895-0.0581.03010.1733-0.5421-0.01020.06640.03680.4733-0.12270.0040.3133-0.00080.253113.85484.463.056
611.60640.97585.49755.44373.142915.3419-0.31430.7267-0.6376-0.3202-0.1084-1.25630.17152.06060.42260.81930.3081-0.2670.41270.08010.6722.49745.06948.66
74.9367-2.56822.09175.34920.99783.39240.1752-0.2892-0.54050.5156-0.08720.29690.5071-0.2961-0.0880.453-0.0256-0.04670.23620.10350.12574.89948.98150.361
85.01310.72121.26474.37620.85592.7790.0032-0.17430.40290.213-0.0372-0.20080.1290.0840.0340.23180.0532-0.00190.28140.02360.143112.7962.75151.705
910.386-5.0037-6.123521.20849.04895.59180.0437-0.47830.6739-1.16620.18290.3562-0.40070.2983-0.22660.2846-0.1669-0.1631.68640.35561.725852.13672.47649.388
102.5543-0.74770.75457.8869-1.32413.68120.00180.2590.4512-0.042-0.2345-2.4135-0.16361.28860.23270.1583-0.02410.03471.01140.03961.268937.99377.02749.615
111.67530.6012-0.32672.8358-0.84524.0118-0.0031-0.1337-0.04410.0217-0.21370.32630.4168-0.60660.21680.0803-0.12690.02580.2213-0.07450.2016-30.72816.802-14.759
124.7372-1.8264-1.16065.54850.89373.64950.1848-0.0698-0.1083-0.0717-0.37660.73270.6174-1.43290.19180.2008-0.34140.03460.6959-0.06970.3843-39.82816.645-8.437
1312.15812.12690.794212.25922.07510.2147-1.65721.27530.9854-1.71961.27941.0503-0.7769-0.07410.37781.16870.3705-0.46030.99150.27421.2563-19.59967.337-14.196
143.07081.31471.99981.06341.37143.0911-0.6888-0.02230.7947-0.872-0.20620.5496-1.4906-0.54560.8951.00430.3591-0.36950.3505-0.02690.771-25.74658.03-8.002
153.4985-0.2535-1.39694.25690.09486.20740.03050.42860.4559-0.9613-0.27040.2802-0.749-0.5860.23990.71550.1413-0.10550.28360.11550.2707-26.93637.638-46.711
162.34310.32041.09461.9161-3.560713.43670.1102-0.0647-0.0487-0.3919-0.10190.7740.4916-1.1984-0.00830.21350.3382-0.25850.9395-0.27461.016-47.8146.835-13.156
174.46040.48560.43463.04920.6053.58060.1842-0.3220.40860.6388-0.2327-0.10980.449-0.09050.04850.2102-0.08390.05580.1590.00690.1878-14.08535.06919.158
182.03621.72451.80661.79892.53654.90070.4021-0.2853-0.04150.5954-0.2934-0.09790.9066-0.3905-0.10870.4558-0.1358-0.04670.22660.08870.33-14.50436.13324.704
193.0917-1.73130.743.9261-2.56781.86350.0949-0.0118-0.19490.34790.02260.5072-0.2754-0.3367-0.11750.19530.02840.02340.9292-0.52190.5916-33.49140.2537.068
201.639-0.93671.71441.4172-2.0213.23950.913-0.2348-0.6409-0.4374-0.41190.1841.37470.495-0.50111.77210.0396-0.40470.43950.09450.6044-3.88822.30518.325
213.52332.19670.91951.38850.44113.6025-0.61220.5013-0.1198-0.40550.3295-0.0473-0.23440.56550.28270.1597-0.13940.0050.16590.05070.2077-6.15839.188-3.314
222.96221.51271.78458.51511.279614.9785-0.3362-1.16181.0062-0.8534-0.85111.0156-1.1057-1.07771.18730.63890.1375-0.16120.5254-0.2490.8076-23.04556.5316.212
231.96123.20050.74156.71392.32051.1256-0.0360.01130.2716-0.671-0.04090.378-0.5282-0.02180.07680.4445-0.0846-0.07370.21980.08130.2572-6.24257.6425.806
242.76081.4064-1.14958.66934.34864.01120.43420.1523-0.0244-0.1009-0.1863-0.5011-0.2620.1165-0.24790.1220.11770.00310.270.04850.1211-10.90933.436-1.206
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 28
2X-RAY DIFFRACTION2A29 - 120
3X-RAY DIFFRACTION3A121 - 254
4X-RAY DIFFRACTION4A255 - 284
5X-RAY DIFFRACTION5A285 - 371
6X-RAY DIFFRACTION6B2 - 28
7X-RAY DIFFRACTION7B29 - 116
8X-RAY DIFFRACTION8B117 - 244
9X-RAY DIFFRACTION9B245 - 266
10X-RAY DIFFRACTION10B267 - 274
11X-RAY DIFFRACTION10B277 - 371
12X-RAY DIFFRACTION11E1 - 307
13X-RAY DIFFRACTION11E501 - 504
14X-RAY DIFFRACTION12E308 - 370
15X-RAY DIFFRACTION13F18 - 49
16X-RAY DIFFRACTION14F50 - 116
17X-RAY DIFFRACTION15F117 - 219
18X-RAY DIFFRACTION16F220 - 274
19X-RAY DIFFRACTION17F275 - 340
20X-RAY DIFFRACTION18F341 - 439
21X-RAY DIFFRACTION18F601 - 603
22X-RAY DIFFRACTION18F604
23X-RAY DIFFRACTION19F440 - 505
24X-RAY DIFFRACTION20G2 - 59
25X-RAY DIFFRACTION21G60 - 114
26X-RAY DIFFRACTION22G115 - 143
27X-RAY DIFFRACTION23G144 - 226
28X-RAY DIFFRACTION24G227 - 283

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