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- PDB-1q1e: The ATPase component of E. coli maltose transporter (MalK) in the... -

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Basic information

Entry
Database: PDB / ID: 1q1e
TitleThe ATPase component of E. coli maltose transporter (MalK) in the nucleotide-free form
ComponentsMaltose/maltodextrin transport ATP-binding protein malK
KeywordsTRANSPORT PROTEIN / ATP-binding cassette / nucleotide-free form / sugar transport
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 / maltose transport complex / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex ...ABC-type maltose transporter / ABC-type maltose transporter activity / negative regulation of maltose transport / enzyme IIA-maltose transporter complex / negative regulation of transmembrane transport / maltose transport complex / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / DNA-binding transcription factor binding / ATP hydrolysis activity / ATP binding / membrane
Similarity search - Function
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 / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Nucleic acid-binding proteins / ABC transporter-like, conserved site ...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 / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Nucleic acid-binding proteins / 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. / 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 / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
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
AuthorsChen, J. / Lu, G. / Lin, J. / Davidson, A.L. / Quiocho, F.A.
CitationJournal: Mol.Cell / Year: 2003
Title: A tweezers-like motion of the ATP-binding cassette dimer in an ABC transport cycle
Authors: Chen, J. / Lu, G. / Lin, J. / Davidson, A.L. / Quiocho, F.A.
History
DepositionJul 19, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltose/maltodextrin transport ATP-binding protein malK
B: Maltose/maltodextrin transport ATP-binding protein malK


Theoretical massNumber of molelcules
Total (without water)84,3692
Polymers84,3692
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.615, 102.041, 99.288
Angle α, β, γ (deg.)90.00, 107.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Maltose/maltodextrin transport 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 OR B4035 OR Z5633 OR ECS5018 / Plasmid: pKPS2E-86 / Production host: Escherichia coli (E. coli) / Strain (production host): HN741 / References: UniProt: P68187

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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: 3.71 Å3/Da / Density % sol: 66.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG5K MME, (NH4)2SO4, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
21 mMATP1drop
31 mMEDTA1drop
410 mMdithiothreitol1drop
520 %glycerol1drop
610 mMsodium citrate1droppH8.
724 %PEG5000 MME1reservoir
80.2 Mammonium sulfate1reservoir
9100 mMMES1reservoirpH6.5

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.98 Å
DetectorDetector: CCD / Date: May 31, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.9→15 Å / Num. all: 27930 / Num. obs: 27930 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 43.9 Å2
Reflection shellResolution: 2.9→3 Å / % possible all: 100
Reflection
*PLUS
Lowest resolution: 20 Å / % possible obs: 99.2 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.117
Reflection shell
*PLUS
% possible obs: 100 % / Redundancy: 5.7 % / Num. unique obs: 2794 / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 6.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→15.78 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 440057.02 / Data cutoff high rms absF: 440057.02 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.276 2143 8 %RANDOM
Rwork0.244 ---
obs0.244 26762 98.2 %-
all-27000 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 22.2848 Å2 / ksol: 0.322701 e/Å3
Displacement parametersBiso mean: 41.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.58 Å20 Å22.51 Å2
2--5.94 Å20 Å2
3----7.52 Å2
Refine analyzeLuzzati coordinate error free: 0.48 Å / Luzzati sigma a free: 0.62 Å
Refinement stepCycle: LAST / Resolution: 2.9→15.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5706 0 0 0 5706
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_improper_angle_d0.97
X-RAY DIFFRACTIONc_mcbond_it1.61.5
X-RAY DIFFRACTIONc_mcangle_it2.772
X-RAY DIFFRACTIONc_scbond_it1.792
X-RAY DIFFRACTIONc_scangle_it2.922.5
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.396 345 8 %
Rwork0.345 3970 -
obs--94.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5ATP_XPLOR_PAR.TXTATP_XPLOR_TOP.TXT
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 20 Å / % reflection Rfree: 5-8
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.97

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