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- PDB-3rlf: Crystal structure of the maltose-binding protein/maltose transpor... -

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Basic information

Entry
Database: PDB / ID: 3rlf
TitleCrystal structure of the maltose-binding protein/maltose transporter complex in an outward-facing conformation bound to MgAMPPNP
Components
  • (Maltose transport system permease protein ...) x 2
  • Maltose-binding periplasmic protein
  • Maltose/maltodextrin import ATP-binding protein MalK
KeywordsHYDROLASE/TRANSPORT PROTEIN / integral membrane protein / ATPase / ABC transporter / membrane / transmembrane / 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 binding / maltose transport complex / maltose transport / maltodextrin transmembrane 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 binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / 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 / ABC transporter-like, conserved site / ABC transporters family signature. / Periplasmic binding protein-like II / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 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: 2.2 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
DepositionApr 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2011Group: Database references
Revision 1.2Sep 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.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 / _atom_site_anisotrop.type_symbol / _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_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 13, 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)220,46215
Polymers215,5675
Non-polymers4,89610
Water6,107339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28580 Å2
ΔGint-188 kcal/mol
Surface area75560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.098, 95.812, 109.983
Angle α, β, γ (deg.)86.70, 82.68, 76.40
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: 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: malE, b4034, JW3994 / Production host: Escherichia coli (E. coli) / Strain (production host): BAR1000 / 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: malK, b4035, JW3995 / Production host: Escherichia coli (E. coli) / Strain (production host): BAR1000 / 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: malF, b4033, JW3993 / Production host: Escherichia coli (E. coli) / Strain (production host): BAR1000 / 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: malG, b4032, JW3992 / Production host: Escherichia coli (E. coli) / Strain (production host): BAR1000 / 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 , 5 types, 348 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 / Phosphatidylglycerol


Mass: 749.007 Da / Num. of mol.: 4 / 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-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
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 339 / 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: 3.4 Å3/Da / Density % sol: 63.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 28% PEG 4000, 0.1M sodium hepes pH 7.5, 0.2M sodium chloride, 0.05M magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 5, 2010
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 127961 / Num. obs: 127961 / % possible obs: 88.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 1.6
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 2 / Rsym value: 0.342 / % possible all: 56.7

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2R6G

2r6g


Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.917 / SU B: 14.118 / SU ML: 0.159 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.272 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25406 6209 5 %RANDOM
Rwork0.2233 ---
all0.22481 117902 --
obs0.22481 117902 86.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.508 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20.56 Å20.83 Å2
2---0.3 Å2-0.85 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14672 0 212 339 15223
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02215267
X-RAY DIFFRACTIONr_angle_refined_deg1.0121.98120752
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.53451900
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.76524.254630
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.156152522
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5991579
X-RAY DIFFRACTIONr_chiral_restr0.0640.22377
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02111342
X-RAY DIFFRACTIONr_mcbond_it0.2521.59435
X-RAY DIFFRACTIONr_mcangle_it0.482215211
X-RAY DIFFRACTIONr_scbond_it0.68535832
X-RAY DIFFRACTIONr_scangle_it1.1494.55538
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 239 -
Rwork0.29 4396 -
obs--43.91 %
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)
11.41780.49030.06363.7677-0.07151.6734-0.0023-0.3798-0.16960.38290.02220.39750.4089-0.2228-0.01980.1889-0.0309-0.00720.27780.1460.214251.807-4.91815.817
21.31270.9257-0.59414.93040.72722.25130.0177-0.4311-0.12280.50280.1668-0.65210.18330.5706-0.18450.13660.0453-0.17380.39310.05910.312368.9833.82316.486
31.40330.31170.29173.19411.31912.8781-0.09370.0665-0.1345-0.2499-0.02430.09640.0181-0.14110.11790.1885-0.0454-0.0370.12070.07630.226756.882-17.891-12.177
45.94850.93930.28467.0140.53674.0534-0.26510.58020.0182-0.93190.04950.26550.3908-0.26690.21560.2905-0.11170.00360.23810.08250.190364.437-6.327-24.243
53.53262.4129-0.68565.9851-0.92282.7134-0.05090.1415-0.1143-0.466-0.0059-0.33730.20680.10180.05680.205-0.02690.00040.10730.00980.196663.704-15.071-16.954
61.89490.14-0.4912.6132-0.21081.53640.0760.0640.1861-0.3250.03870.0194-0.3107-0.0718-0.11470.201-0.0381-0.03630.15130.07950.168757.17321.193-3.573
73.1449-0.883-0.53932.08830.39011.09440.04370.11390.0486-0.1719-0.0157-0.2844-0.14910.0699-0.0280.1337-0.1160.00790.19150.07190.286673.29710.962-9.8
85.60523.6461-1.14734.9709-1.29282.6520.0544-0.3398-0.58630.0025-0.2312-1.15550.20830.74430.17680.03430.0342-0.0250.36620.07370.583690.463-2.136-8.016
91.4939-0.7068-1.5052.59561.3164.83160.12790.2778-0.21080.0036-0.37510.208-0.2776-0.68090.24720.08290.0247-0.0470.2825-0.00460.1423.87852.67964.68
104.1318-0.1921-1.39452.91410.72613.89590.63630.37450.3948-0.4363-0.59590.3048-1.647-1.1916-0.04041.00130.80290.01930.74670.06930.206115.42172.10340.316
110.8924-0.274-0.50980.91660.30993.87180.38220.20550.0637-0.0895-0.37030.0818-1.1616-1.017-0.01190.47290.36320.0230.43530.0050.171320.14964.87952.563
1211.348-9.6065-10.16039.1018.40814.0229-1.3242-1.84280.35591.73181.29020.23542.60311.28880.03391.5230.04430.6570.5222-0.07620.531437.68310.90555.285
130.7177-0.5195-1.55581.11631.24373.5097-0.10850.4-0.25740.1819-0.41890.3290.2596-0.81580.52740.0545-0.111-0.00320.3549-0.10220.287419.9440.58259.288
140.6715-0.7335-1.50791.25681.57383.42980.14150.5062-0.169-0.3667-0.51070.1912-0.3246-1.24710.36920.20120.1702-0.13210.7363-0.09420.244328.12541.03523.794
150.8151-1.1232-1.07122.45812.12974.1570.25050.00960.1757-0.2477-0.0286-0.3621-0.80420.0652-0.2220.2176-0.02620.02830.23630.07780.249945.76449.52636.328
164.19521.11342.12525.05026.194610.9563-0.07530.0704-0.59720.9013-0.47610.51451.3268-0.68980.55140.296-0.19860.18860.2438-0.06340.369230.38525.01244.497
170.4273-0.8637-1.11282.33422.54123.0614-0.00160.0029-0.03980.0489-0.08290.07910.0701-0.08920.08450.1667-0.0075-0.03290.24330.05940.221544.98232.27435.584
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 94
2X-RAY DIFFRACTION1A1501
3X-RAY DIFFRACTION1A2501
4X-RAY DIFFRACTION2A95 - 194
5X-RAY DIFFRACTION3A195 - 291
6X-RAY DIFFRACTION4A292 - 329
7X-RAY DIFFRACTION5A330 - 372
8X-RAY DIFFRACTION6B2 - 167
9X-RAY DIFFRACTION6B1502
10X-RAY DIFFRACTION6B2502
11X-RAY DIFFRACTION7B168 - 248
12X-RAY DIFFRACTION8B249 - 372
13X-RAY DIFFRACTION9E1 - 114
14X-RAY DIFFRACTION10E115 - 216
15X-RAY DIFFRACTION11E217 - 374
16X-RAY DIFFRACTION11E5004
17X-RAY DIFFRACTION12F10 - 57
18X-RAY DIFFRACTION13F58 - 344
19X-RAY DIFFRACTION14F345 - 503
20X-RAY DIFFRACTION14F2000
21X-RAY DIFFRACTION14F4001
22X-RAY DIFFRACTION15G11 - 114
23X-RAY DIFFRACTION16G115 - 155
24X-RAY DIFFRACTION17G156 - 296
25X-RAY DIFFRACTION17F4002
26X-RAY DIFFRACTION17G4006
27X-RAY DIFFRACTION17G4009

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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