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- PDB-3fh6: Crystal structure of the resting state maltose transporter from E... -

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Basic information

Entry
Database: PDB / ID: 3fh6
TitleCrystal structure of the resting state maltose transporter from E. coli
Components
  • Maltose transport system permease protein malF
  • Maltose transport system permease protein malG
  • Maltose/maltodextrin import ATP-binding protein malK
KeywordsTRANSPORT PROTEIN / maltose transporter / ground state / ABC transporter / membrane protein / Cell inner membrane / Cell membrane / Membrane / Sugar transport / Transmembrane / Transport / ATP-binding / Hydrolase / Nucleotide-binding
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 / DNA damage response / ATP hydrolysis activity / ATP binding / membrane / plasma membrane
Similarity search - Function
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. / Transport-associated OB, type 2 / TOBE domain / MalK OB fold domain ...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. / 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. / 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. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Maltose/maltodextrin transport system permease protein MalF / 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 / MAD / Resolution: 4.5 Å
AuthorsKhare, D. / Oldham, M.L. / Orelle, C. / Davidson, A.L. / Chen, J.
CitationJournal: Mol.Cell / Year: 2009
Title: Alternating access in maltose transporter mediated by rigid-body rotations.
Authors: Khare, D. / Oldham, M.L. / Orelle, C. / Davidson, A.L. / Chen, J.
History
DepositionDec 8, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 6, 2023Group: Data collection / Database references / 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
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

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Assembly

Deposited unit
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
H: Maltose transport system permease protein malF
I: Maltose transport system permease protein malG
C: Maltose/maltodextrin import ATP-binding protein malK
D: Maltose/maltodextrin import ATP-binding protein malK


Theoretical massNumber of molelcules
Total (without water)339,4178
Polymers339,4178
Non-polymers00
Water0
1
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


Theoretical massNumber of molelcules
Total (without water)169,7084
Polymers169,7084
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10930 Å2
ΔGint-112 kcal/mol
Surface area62150 Å2
MethodPISA
2
H: Maltose transport system permease protein malF
I: Maltose transport system permease protein malG
C: Maltose/maltodextrin import ATP-binding protein malK
D: Maltose/maltodextrin import ATP-binding protein malK


Theoretical massNumber of molelcules
Total (without water)169,7084
Polymers169,7084
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10940 Å2
ΔGint-112 kcal/mol
Surface area62150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.097, 209.480, 438.741
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.88774, 0.08265, 0.45286), (-0.09761, 0.99518, 0.00972), (-0.44987, -0.05283, 0.89153)
Vector: 24.0031, -64.79521, -0.99527)

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Components

#1: Protein Maltose transport system permease protein malF


Mass: 53093.113 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b4033, JW3993, malF / Production host: Escherichia coli (E. coli) / References: UniProt: P02916
#2: Protein Maltose transport system permease protein malG


Mass: 32246.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b4032, JW3992, malG / Production host: Escherichia coli (E. coli) / References: UniProt: P68183
#3: Protein
Maltose/maltodextrin import 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: K-12 / Gene: b4035, JW3995, malK / Production host: Escherichia coli (E. coli) / References: UniProt: P68187, EC: 3.6.3.19

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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: 5.79 Å3/Da / Density % sol: 78.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 11.5 % PEG 4000, 0.1M ADA pH 6.5, 0.1 M NaCl, 0.1 M Li2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97942, 0.9794, 0.9795, 0.9494
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 10, 2007
RadiationMonochromator: Si(111) double crystal / Protocol: MAD / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979421
20.97941
30.97951
40.94941
ReflectionResolution: 4.5→100 Å / Num. obs: 40160 / % possible obs: 87.5 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.126 / Χ2: 1.975 / Net I/σ(I): 11.126
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
4.5-4.662.50.78430222.038169.1
4.66-4.852.70.81531581.959172.2
4.85-5.072.80.68132952.001175.1
5.07-5.342.90.59934021.991177.8
5.34-5.673.10.61139252189.5
5.67-6.113.60.57143111.849197.7
6.11-6.723.90.37244101.956199.7
6.72-7.6940.21444252.245199.5
7.69-9.693.90.1144461.914199.3
9.69-1003.80.08643671.83193.9

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
DMphasing
CNSrefinement
PDB_EXTRACT3.006data extraction
MAR345CCDdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MAD
Starting model: PDB entries 1Q1B, 1Q1E, 2R6G

1q1b

1q1e

2r6g


Resolution: 4.5→50 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
Details: The structure was refined with strict NCS restraints applied to the refined molecules F,G,A,B. The molecules H,I,C,D that build the complete asymmetric unit, are the respective NCS-mates
RfactorNum. reflection% reflection
Rfree0.363 2012 4.3 %
Rwork0.34 --
obs-38761 85.2 %
Solvent computationBsol: 137.42 Å2
Displacement parametersBiso max: 521.43 Å2 / Biso mean: 300.466 Å2 / Biso min: 94.21 Å2
Refinement stepCycle: LAST / Resolution: 4.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20236 0 0 0 20236
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.998
Xplor fileSerial no: 1 / Param file: protein_between.param

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