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

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Basic information

Entry
Database: PDB / ID: 3pux
TitleCrystal Structure of an outward-facing MBP-Maltose transporter complex bound to ADP-BeF3
Components
  • (Maltose transport system permease protein ...) x 2
  • Maltose-binding periplasmic protein
  • Maltose/maltodextrin import ATP-binding protein MalK
KeywordsHYDROLASE/TRANSPORT PROTEIN / ATP Binding Cassette / Nucleotide Binding Domain / Substrate Binding Protein / ABC Transporter / importer / ATPase / ATP binding / Maltodextrin binding / transmembrane integral membrane / 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 transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding ...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 / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / 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. / D-Maltodextrin-Binding Protein; domain 2 / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / P-loop containing nucleotide triphosphate hydrolases / Nucleic acid-binding, OB-fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / 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 / ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / 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: 2.3 Å
AuthorsOldham, M.L. / Chen, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Snapshots of the maltose transporter during ATP hydrolysis.
Authors: Oldham, M.L. / Chen, J.
History
DepositionDec 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2011Group: Database references
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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _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.id / _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_asym_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.src_method / _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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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-binding periplasmic protein
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,65423
Polymers215,2905
Non-polymers9,36418
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34910 Å2
ΔGint-280 kcal/mol
Surface area76030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.130, 97.340, 112.840
Angle α, β, γ (deg.)85.58, 78.98, 72.25
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-binding periplasmic protein / MMBP / Maltodextrin-binding protein


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: b4034, ECDH10B_4223, JW3994, malE / Plasmid: pJF2 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9
#4: Protein Maltose/maltodextrin import ATP-binding protein MalK


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: b4035, ECDH10B_4224, JW3995, malK / Plasmid: pKJ / Production host: Escherichia coli (E. coli) / References: UniProt: P68187, EC: 3.6.3.19

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

#2: 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: b4033, ECDH10B_4222, JW3993, malF / Plasmid: pFG23 / Production host: Escherichia coli (E. coli) / References: UniProt: P02916
#3: 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: b4032, ECDH10B_4221, JW3992, malG / Plasmid: pFG23 / Production host: Escherichia coli (E. coli) / References: UniProt: P68183

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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 , 6 types, 269 molecules

#6: Chemical ChemComp-UMQ / UNDECYL-MALTOSIDE / UNDECYL-BETA-D-MALTOPYRANOSIDE


Mass: 496.589 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H44O11 / Comment: detergent*YM
#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


Mass: 749.007 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C40H77O10P / Comment: phospholipid*YM
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#9: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#10: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BeF3
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 3.92 Å3/Da / Density % sol: 68.59 %
Crystal growTemperature: 293 K / pH: 7.5
Details: 27% PEG 400, 0.1 M HEPES, 10 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: 0.97965
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: 0.97965 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 91147 / % possible obs: 59.7 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.055
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1.9 / Rsym value: 0.451 / % possible all: 16.8

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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: 2.3→19.81 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.885 / SU B: 16.402 / SU ML: 0.181 / Cross valid method: THROUGHOUT / ESU R: 0.455 / ESU R Free: 0.297 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.265 4725 5 %RANDOM
Rwork0.228 ---
obs0.23 89108 64.8 %-
all-91147 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.32 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20.35 Å20.26 Å2
2--0.05 Å20 Å2
3----0.43 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14638 0 260 252 15150
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02215362
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3061.98320872
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.53551917
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.79724.263631
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.621152546
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3131579
X-RAY DIFFRACTIONr_chiral_restr0.0860.22391
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02111390
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_it0.4891.59457
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.918215269
X-RAY DIFFRACTIONr_scbond_it1.35535905
X-RAY DIFFRACTIONr_scangle_it2.2454.55591
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 101 -
Rwork0.269 1679 -
obs--16.83 %
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)
10.4708-0.2133-0.09152.72081.55572.03060.0053-0.0365-0.0692-0.01880.0836-0.1210.36480.1189-0.08890.1516-0.00350.0060.07970.04970.102-9.69-9.29736.4249
21.1102-0.6783-0.51782.11470.64281.48040.03610.04970.1844-0.59610.1552-0.5424-0.11770.1988-0.19130.2063-0.05660.17570.11830.00680.22141.99837.9733-1.5311
30.3789-0.2709-0.04441.21660.00053.07680.1554-0.02750.03840.0051-0.28730.1674-0.7161-0.58870.13190.28630.1354-0.03540.2525-0.13630.2014-47.308961.658159.0082
40.31-0.3579-0.75791.00850.84732.2855-0.0630.1735-0.11870.0742-0.27280.20690.196-0.42650.33570.0504-0.0753-0.01530.1877-0.07730.194-43.224136.249153.2911
50.7049-0.8748-0.6382.34481.47542.4164-0.0085-0.0450.0749-0.018-0.0327-0.0655-0.05580.05190.04120.0215-0.0397-0.03580.1110.02870.1398-23.8735.96342.4758
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 372
2X-RAY DIFFRACTION1A1501
3X-RAY DIFFRACTION1A2501
4X-RAY DIFFRACTION1A3001
5X-RAY DIFFRACTION1A382 - 383
6X-RAY DIFFRACTION2B2 - 369
7X-RAY DIFFRACTION2B1502
8X-RAY DIFFRACTION2B2502
9X-RAY DIFFRACTION2B3002
10X-RAY DIFFRACTION2B382 - 383
11X-RAY DIFFRACTION3E1 - 374
12X-RAY DIFFRACTION4F10 - 503
13X-RAY DIFFRACTION4F2000
14X-RAY DIFFRACTION4F4001
15X-RAY DIFFRACTION4F4010
16X-RAY DIFFRACTION5G2 - 296
17X-RAY DIFFRACTION5G4003 - 4009
18X-RAY DIFFRACTION5F4002 - 4008

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