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- PDB-3puz: Crystal Structure of a pre-translocation state MBP-Maltose transp... -

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Entry
Database: PDB / ID: 3puz
TitleCrystal Structure of a pre-translocation state MBP-Maltose transporter complex bound to AMP-PNP
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 / 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 / Maltose/Maltodextrin import ATP-binding protein malK family profile. / MetI-like fold / MetI-like / 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 / 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 / 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: 2.9 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 / 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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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)216,97812
Polymers214,4845
Non-polymers2,4957
Water1448
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24320 Å2
ΔGint-179 kcal/mol
Surface area78710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.021, 93.360, 119.761
Angle α, β, γ (deg.)90.05, 102.57, 105.01
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: 40815.305 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: pJF1 / 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, 2 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.: 2
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, 13 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.: 8 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.93 Å3/Da / Density % sol: 68.66 %
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: 1.03326 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: 1.03326 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 53826 / Num. obs: 53826 / % possible obs: 71.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.043
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 1.7 / Rsym value: 0.417 / % possible all: 23.6

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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 / Resolution: 2.9→19.95 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.874 / SU B: 46.195 / SU ML: 0.38 / Cross valid method: THROUGHOUT / ESU R Free: 0.474 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27878 2864 5.2 %RANDOM
Rwork0.23716 ---
obs0.23928 52679 77 %-
all-53826 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 92.327 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-0.02 Å2-0.04 Å2
2--0.09 Å2-0.12 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.9→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14536 0 153 8 14697
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02215013
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8941.9820411
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.21651867
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.79824.251621
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.065152494
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5681578
X-RAY DIFFRACTIONr_chiral_restr0.0580.22348
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02111171
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_it0.1441.59312
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.267215013
X-RAY DIFFRACTIONr_scbond_it0.25835701
X-RAY DIFFRACTIONr_scangle_it0.4624.55398
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
Rfree0.396 74 -
Rwork0.335 1468 -
obs--29.08 %
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)
10.9517-0.10360.11174.17593.99366.9496-0.09530.02110.0571-0.18490.1509-0.4932-0.48350.1631-0.05560.5302-0.1454-0.04220.13690.11550.373831.202-5.72642.725
24.48940.33392.20766.55151.51754.47610.0054-0.32190.1540.7519-0.1119-0.26790.4215-0.24690.10650.61390.122-0.12090.2520.04890.093830.03-34.46552.453
36.2126-6.40651.269912.9645-1.15646.00540.21230.22091.2245-0.0839-0.3574-3.5056-0.71271.87410.14510.4815-0.2546-0.22251.17810.05352.036259.7-13.66250.621
41.83410.4255-0.1852.8476-1.01214.4940.0843-0.22910.0065-0.2157-0.16110.65830.8015-0.87670.07680.1744-0.176-0.00110.3392-0.09640.3193-12.537-72.924-13.214
515.40758.063811.124413.14457.789813.5239-2.05211.70052.2146-3.54160.95142.7374-2.7569-0.17471.10072.47630.2545-0.8170.83420.31151.44282.95-19.315-9.246
60.55660.28160.91351.86611.10784.7933-0.0026-0.26220.2601-0.2067-0.38740.488-0.3155-0.91050.390.06850.11830.03920.3561-0.04590.4033-5.734-49.431-3.818
71.64281.79270.97533.98021.78153.7533-0.06290.0180.0737-0.17360.0980.0848-0.33670.1615-0.03510.11960.02270.11880.2905-0.0490.188612.383-45.9547.253
80.59771.5434-0.57239.50713.00144.77790.1653-0.03180.04030.03050.0316-0.2578-0.18060.4352-0.19690.13330.03680.08020.3551-0.01280.22289.68-54.4720.483
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 371
2X-RAY DIFFRACTION1A2501
3X-RAY DIFFRACTION1A1501
4X-RAY DIFFRACTION2B2 - 228
5X-RAY DIFFRACTION2B2502
6X-RAY DIFFRACTION2B1502
7X-RAY DIFFRACTION3B229 - 371
8X-RAY DIFFRACTION4E1 - 370
9X-RAY DIFFRACTION4E2002
10X-RAY DIFFRACTION5F18 - 64
11X-RAY DIFFRACTION6F65 - 503
12X-RAY DIFFRACTION6F4001
13X-RAY DIFFRACTION6F2001
14X-RAY DIFFRACTION7G2 - 216
15X-RAY DIFFRACTION8G217 - 283

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