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- PDB-3pv0: Crystal Structure of a pre-translocation state MBP-Maltose transp... -

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Entry
Database: PDB / ID: 3pv0
TitleCrystal Structure of a pre-translocation state MBP-Maltose transporter complex without nucleotide
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 / 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 / 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 / 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 2.1Sep 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
Revision 2.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)215,9178
Polymers214,4845
Non-polymers1,4343
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22620 Å2
ΔGint-149 kcal/mol
Surface area78720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.543, 92.630, 119.132
Angle α, β, γ (deg.)90.48, 102.13, 104.21
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 / 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.: 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
#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

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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: 3.82 Å3/Da / Density % sol: 67.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 32% PEG 400, 0.1M HEPES, 40 mM magnesium chloride, 50mM 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: 0.96863 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: 0.96863 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 41826 / Num. obs: 41826 / % possible obs: 68.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.062
Reflection shellResolution: 3→3.16 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.5 / Rsym value: 0.44 / % possible all: 17.5

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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→19.96 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.871 / SU B: 54.196 / SU ML: 0.419 / Cross valid method: THROUGHOUT / ESU R Free: 0.565 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27356 2229 5.1 %RANDOM
Rwork0.23096 ---
obs0.23313 41181 75.57 %-
all-41826 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 83.751 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20.36 Å20.86 Å2
2--0.81 Å20.3 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 3.1→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14546 0 97 0 14643
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.02214968
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.6431.97620341
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.83151869
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.03524.251621
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.888152494
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9471578
X-RAY DIFFRACTIONr_chiral_restr0.0450.22342
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02111169
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_it0.27229325
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.487315033
X-RAY DIFFRACTIONr_scbond_it0.13925643
X-RAY DIFFRACTIONr_scangle_it0.23435308
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
Rfree0.382 54 -
Rwork0.335 1009 -
obs--25.42 %
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)
10.51160.23910.12042.99432.84816.264-0.2101-0.03650.1266-0.13630.1311-0.3204-0.49190.10910.0790.3267-0.0754-0.11220.08090.01670.190928.503-5.56144.157
215.65579.67275.499910.11273.29231.9623-0.94540.97090.01980.12860.7855-1.753-0.22660.46550.15991.36020.746-0.56770.6347-0.17710.79838.92-40.52652.097
33.39010.43571.48583.36421.72853.06420.1038-0.2050.11540.606-0.1645-0.09670.5373-0.23420.06080.48330.1046-0.06640.18640.0340.058924.68-32.99654.564
44.3773-1.79720.66548.7316-1.67335.41210.02760.27880.4187-0.1752-0.2247-2.0845-0.32371.47130.19710.1503-0.037-0.14530.8455-0.1450.844156.846-13.70252.015
51.29960.6587-0.38852.8536-0.55214.43690.0318-0.16430.0511-0.1554-0.31470.36130.6504-0.91910.28290.1177-0.14880.01040.3078-0.14810.2488-15.622-72.437-11.505
60.34890.43610.89611.9281.33024.6031-0.311-0.20850.3659-0.9595-0.44720.6395-1.2387-0.95050.75820.60740.3988-0.32290.3629-0.1220.4764-12.81-41.168-19.432
71.06480.46731.07261.52651.79314.5850.1753-0.11630.0710.525-0.4270.08640.3979-0.58440.25160.2284-0.10550.06930.2361-0.02120.1791-1.313-52.63320.585
81.64341.60461.16474.06133.32895.53770.14680.0925-0.47470.2630.1635-0.44270.77830.3312-0.31030.1610.030.01410.0532-0.07730.250212.126-60.0559.833
95.57283.75382.26687.29682.10153.8665-0.3375-0.22490.7943-0.5151-0.60851.4211-1.1816-0.52260.9460.48140.2263-0.1660.1436-0.10290.5375-3.699-32.2193.057
101.32992.97011.32227.3393.3822.84010.0456-0.0181-0.0749-0.1408-0.1124-0.1635-0.3952-0.10710.06680.18310.00580.01890.1751-0.00220.13279.96-42.1236.931
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 371
2X-RAY DIFFRACTION2B2 - 28
3X-RAY DIFFRACTION3B29 - 228
4X-RAY DIFFRACTION4B229 - 371
5X-RAY DIFFRACTION5E1 - 370
6X-RAY DIFFRACTION5E2002
7X-RAY DIFFRACTION6F18 - 297
8X-RAY DIFFRACTION7F298 - 505
9X-RAY DIFFRACTION7F2001
10X-RAY DIFFRACTION8G2 - 112
11X-RAY DIFFRACTION9G113 - 154
12X-RAY DIFFRACTION10G155 - 283

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