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- PDB-1q12: Crystal Structure of the ATP-bound E. coli MalK -

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Basic information

Entry
Database: PDB / ID: 1q12
TitleCrystal Structure of the ATP-bound E. coli MalK
ComponentsMaltose/maltodextrin transport ATP-binding protein malK
KeywordsTRANSPORT PROTEIN / ATP-binding cassette
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 / Nucleic acid-binding, OB-fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Maltose/maltodextrin import ATP-binding protein MalK
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 18, 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 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
C: Maltose/maltodextrin transport ATP-binding protein malK
D: Maltose/maltodextrin transport ATP-binding protein malK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,7678
Polymers168,7384
Non-polymers2,0294
Water18010
1
A: Maltose/maltodextrin transport ATP-binding protein malK
B: Maltose/maltodextrin transport ATP-binding protein malK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,3834
Polymers84,3692
Non-polymers1,0142
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-22 kcal/mol
Surface area31420 Å2
MethodPISA
2
C: Maltose/maltodextrin transport ATP-binding protein malK
D: Maltose/maltodextrin transport ATP-binding protein malK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,3834
Polymers84,3692
Non-polymers1,0142
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-23 kcal/mol
Surface area31310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.880, 97.278, 101.862
Angle α, β, γ (deg.)74.59, 82.47, 76.85
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Maltose/maltodextrin transport ATP-binding protein malK


Mass: 42184.535 Da / Num. of mol.: 4
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
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 3.29 Å3/Da / Density % sol: 62.62 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: PEG 4000, glycerol, Sodium Acetate, Tris, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 273K
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
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 12, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.6→15 Å / Num. all: 138796 / Num. obs: 124917 / % possible obs: 90 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Biso Wilson estimate: 20.5 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.106 / Net I/σ(I): 18.5
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 2 % / Rmerge(I) obs: 0.283 / Mean I/σ(I) obs: 5.4 / Num. unique all: 8481 / Rsym value: 0.283 / % possible all: 61
Reflection
*PLUS
Lowest resolution: 15 Å / % possible obs: 89.9 % / Rmerge(I) obs: 0.106
Reflection shell
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 2.7 Å / % possible obs: 60.1 % / Redundancy: 2.1 % / Num. unique obs: 8481

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G29

1g29


Resolution: 2.6→14.8 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 613412.44 / Data cutoff high rms absF: 613412.44 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.286 8916 7.8 %RANDOM
Rwork0.258 ---
obs0.258 113764 86.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.6054 Å2 / ksol: 0.331177 e/Å3
Displacement parametersBiso mean: 70.1 Å2
Baniso -1Baniso -2Baniso -3
1-19.38 Å2-21.97 Å2-22.93 Å2
2---10.51 Å210.44 Å2
3----8.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.44 Å
Luzzati d res low-5 Å
Luzzati sigma a0.57 Å0.54 Å
Refinement stepCycle: LAST / Resolution: 2.6→14.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11412 0 124 10 11546
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_improper_angle_d1.02
X-RAY DIFFRACTIONc_mcbond_it1.581.5
X-RAY DIFFRACTIONc_mcangle_it2.772
X-RAY DIFFRACTIONc_scbond_it1.952
X-RAY DIFFRACTIONc_scangle_it3.142.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.42 1065 7.9 %
Rwork0.388 12451 -
obs--61.5 %
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: 2.6 Å / Lowest resolution: 15 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_deg24.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.02

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