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- PDB-3puy: Crystal Structure of an outward-facing MBP-Maltose transporter co... -

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Basic information

Entry
Database: PDB / ID: 3puy
TitleCrystal Structure of an outward-facing MBP-Maltose transporter complex bound to AMP-PNP after crystal soaking of the pretranslocation state
Components
  • (Maltose transporter subunit; membrane component of ABC ...) x 2
  • Fused maltose transport subunit, ATP-binding component of ABC superfamily; regulatory protein
  • Maltose transporter subunit; periplasmic-binding component of ABC superfamily
KeywordsTRANSPORT PROTEIN / MEMBRANE PROTEIN / ATP Binding Cassette / Nucleotide Binding Domain / Substrate Binding Protein / ABC Transporter / importer / ATPase / ATP binding / Maltodextrin binding / transmembrane integral membrane
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 transport complex / maltose binding / carbohydrate transport / maltose 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 transport complex / maltose binding / carbohydrate transport / maltose transport / maltodextrin transmembrane 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 / 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 / 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 / Periplasmic binding protein-like II / 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. / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Chem-PGV / : / : / : / : / 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
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsOldham, M.L. / Chen, J.
CitationJournal: Science / Year: 2011
Title: Crystal structure of the maltose transporter in a pretranslocation intermediate state.
Authors: Oldham, M.L. / Chen, J.
History
DepositionDec 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
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 / 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_conn_angle / struct_conn / struct_conn_type / 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_atom_id / _atom_site.label_comp_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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 transporter subunit; periplasmic-binding component of ABC superfamily
F: Maltose transporter subunit; membrane component of ABC superfamily
G: Maltose transporter subunit; membrane component of ABC superfamily
A: Fused maltose transport subunit, ATP-binding component of ABC superfamily; regulatory protein
B: Fused maltose transport subunit, ATP-binding component of ABC superfamily; regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,44311
Polymers215,2905
Non-polymers2,1526
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26970 Å2
ΔGint-178 kcal/mol
Surface area75960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.550, 96.283, 112.283
Angle α, β, γ (deg.)86.91, 80.87, 74.32
Int Tables number1
Space group name H-MP1

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Components

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Protein , 2 types, 3 molecules EAB

#1: Protein Maltose transporter subunit; periplasmic-binding component of ABC superfamily


Mass: 41622.047 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: ECDH10B_4223, malE / Plasmid: pJF2 / Production host: Escherichia coli (E. coli) / References: UniProt: B1XC33, UniProt: P0AEX9*PLUS
#4: Protein Fused maltose transport subunit, ATP-binding component of ABC superfamily; regulatory protein


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 / Gene: ECDH10B_4224, malK / Plasmid: pKJ / Production host: Escherichia coli (E. coli) / References: UniProt: B1XC34, UniProt: P68187*PLUS

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Maltose transporter subunit; membrane component of ABC ... , 2 types, 2 molecules FG

#2: Protein Maltose transporter subunit; membrane component of ABC superfamily


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: ECDH10B_4222, malF / Plasmid: pFG23 / Production host: Escherichia coli (E. coli) / References: UniProt: B1XC32, UniProt: P02916*PLUS
#3: Protein Maltose transporter subunit; membrane component of ABC superfamily


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: ECDH10B_4221, malG / Plasmid: pFG23 / Production host: Escherichia coli (E. coli) / References: UniProt: B1XC31, UniProt: P68183*PLUS

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Sugars , 1 types, 1 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

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Non-polymers , 4 types, 16 molecules

#6: 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


Mass: 749.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H77O10P / Comment: phospholipid*YM
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 66.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 32% PEG 400, 0.1 M HEPES, 40 mM magnesium chloride, 50 mM sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03324 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 10, 2009
RadiationMonochromator: double crystal monochromator and vertically focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03324 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 46613 / Num. obs: 46613 / % possible obs: 64.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.061
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 1.5 % / Mean I/σ(I) obs: 1.3 / Rsym value: 0.532 / % possible all: 23.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2R6G

2r6g


Resolution: 3.1→20 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.885 / SU B: 48.934 / SU ML: 0.377 / Cross valid method: THROUGHOUT / ESU R Free: 0.5 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25427 2301 5.1 %RANDOM
Rwork0.21426 ---
obs0.21629 43231 82.69 %-
all-46613 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 81.172 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å20.21 Å20.19 Å2
2--0.63 Å2-0.2 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 3.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14640 0 138 11 14789
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02215104
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0111.97820533
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.65551877
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.35724.281626
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.059152507
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9531577
X-RAY DIFFRACTIONr_chiral_restr0.0650.22350
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02111252
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.2481.59371
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.463215096
X-RAY DIFFRACTIONr_scbond_it0.4535733
X-RAY DIFFRACTIONr_scangle_it0.8154.55437
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.179 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 97 -
Rwork0.321 1711 -
obs--45.52 %
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)
10.7535-0.1561-0.07743.10291.67412.42730.0208-0.0571-0.1035-0.1617-0.0573-0.21950.30620.01410.03660.56720.05290.0070.34610.07470.362569.494-6.0074.084
24.4717-0.3778-0.80092.55580.02752.0710.26740.2630.2905-0.847-0.1758-0.2783-0.3598-0.1973-0.09160.70250.04660.15580.35110.10350.328370.97719.249-2.601
30.84747.6676-1.329521.12168.026518.13940.11860.5676-1.35390.68643.1193-4.9134-0.1510.6834-3.2380.34190.54450.63281.8526-0.092.2578109.6272.251-8.951
45.26723.8384-0.14128.7401-2.29832.21410.62780.1372-0.8299-0.7863-0.3881-2.05010.17330.6335-0.23960.62280.31290.42040.5449-0.05770.972995.529-4.46-4.82
53.5642-1.0321-0.80514.45550.97055.2302-0.0309-0.0001-0.14180.3172-0.13190.0299-0.1542-0.45440.16280.3921-0.0452-0.05260.4134-0.07330.343533.61752.88969.104
65.26430.9483-1.0673.64140.15093.3080.49680.57860.48-0.2399-0.41940.2511-1.357-1.0276-0.07740.82770.6037-0.04550.58060.0740.423626.03573.10245.013
71.1967-0.1934-1.19241.97520.4094.71180.30680.21110.24490.1704-0.2390.0432-0.9161-0.7618-0.06790.47410.2394-0.04090.4116-0.04880.441629.74965.22757.446
89.2006-1.8514-3.52468.68110.16296.5905-0.5068-1.3743-0.07910.82780.37220.46791.17520.6240.13461.142-0.24070.34960.5840.09040.36848.23411.52558.746
90.6551-0.6112-0.94011.68380.98193.376-0.19770.2596-0.15880.5367-0.27060.33420.4864-0.82370.46830.3523-0.23510.0350.4444-0.11230.448928.6939.4666.257
101.088-0.9629-1.30011.29530.96453.28420.11550.4393-0.0414-0.3638-0.39250.0651-0.1992-0.87060.2770.33690.0279-0.11240.6756-0.02210.432139.46544.02328.806
111.2446-0.478-0.59893.61511.31423.88060.27180.03110.3438-0.1094-0.0825-0.5962-0.69670.284-0.18930.2606-0.1255-0.01310.32480.06650.607956.92551.05538.651
124.4917-2.8707-2.10965.65214.295610.9653-0.13530.1102-0.72050.2299-0.88010.63330.0962-0.85151.01540.5326-0.30350.12560.3298-0.02960.737941.31924.81647.272
131.4541-1.679-1.23313.44912.16453.00920.11640.04710.1243-0.0013-0.2011-0.04610.15250.01680.08470.3454-0.1101-0.0730.40530.07080.460955.40733.25439.662
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 372
2X-RAY DIFFRACTION1A1501
3X-RAY DIFFRACTION1A2501
4X-RAY DIFFRACTION1A382 - 383
5X-RAY DIFFRACTION2B2 - 241
6X-RAY DIFFRACTION2B1502
7X-RAY DIFFRACTION2B2502
8X-RAY DIFFRACTION2B382 - 383
9X-RAY DIFFRACTION3B242 - 271
10X-RAY DIFFRACTION4B280 - 369
11X-RAY DIFFRACTION5E1 - 113
12X-RAY DIFFRACTION6E114 - 219
13X-RAY DIFFRACTION7E220 - 374
14X-RAY DIFFRACTION8F10 - 57
15X-RAY DIFFRACTION9F58 - 319
16X-RAY DIFFRACTION10F320 - 503
17X-RAY DIFFRACTION10F2001
18X-RAY DIFFRACTION10F4001
19X-RAY DIFFRACTION11G2 - 112
20X-RAY DIFFRACTION12G113 - 155
21X-RAY DIFFRACTION13G156 - 296

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