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- PDB-3dhw: Crystal structure of methionine importer MetNI -

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Basic information

Entry
Database: PDB / ID: 3dhw
TitleCrystal structure of methionine importer MetNI
Components
  • D-methionine transport system permease protein metI
  • Methionine import ATP-binding protein metN
KeywordsMEMBRANE PROTEIN/HYDROLASE / ABC-transporter / Methionine uptake transporter / membrane protein / Amino-acid transport / Inner membrane / Transmembrane / ATP-binding / Hydrolase / Nucleotide-binding / MEMBRANE PROTEIN-HYDROLASE COMPLEX
Function / homology
Function and homology information


L-methionine transmembrane transporter activity / ABC-type D-methionine transporter activity / methionine import across plasma membrane / methionine-importing ABC transporter complex / ABC-type methionine transporter / D-methionine transmembrane transport / Gram-negative-bacterium-type cell wall / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATPase-coupled transmembrane transporter activity / metabolic process ...L-methionine transmembrane transporter activity / ABC-type D-methionine transporter activity / methionine import across plasma membrane / methionine-importing ABC transporter complex / ABC-type methionine transporter / D-methionine transmembrane transport / Gram-negative-bacterium-type cell wall / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATPase-coupled transmembrane transporter activity / metabolic process / ATP hydrolysis activity / ATP binding / membrane / plasma membrane
Similarity search - Function
ABC transporter, methionine import, ATP-binding protein MetN, proteobacteria / NIL domain / NIL domain / Methionine import ATP-binding protein metN family profile. / NIL / Methionine import ATP-binding protein MetN, ATP-binding domain / MetI-like fold / MetI-like / ABC transporter type 1, transmembrane domain MetI-like / MetI-like superfamily ...ABC transporter, methionine import, ATP-binding protein MetN, proteobacteria / NIL domain / NIL domain / Methionine import ATP-binding protein metN family profile. / NIL / Methionine import ATP-binding protein MetN, ATP-binding domain / MetI-like fold / MetI-like / 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. / ACT domain / ACT-like domain / 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. / P-loop containing nucleotide triphosphate hydrolases / Alpha-Beta Plaits / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Methionine import ATP-binding protein MetN / D-methionine transport system permease protein MetI
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.7 Å
AuthorsRees, D.C. / Kaiser, J.T. / Kadaba, N.S. / Johnson, E. / Lee, A.T.
CitationJournal: Science / Year: 2008
Title: The high-affinity E. coli methionine ABC transporter: structure and allosteric regulation.
Authors: Kadaba, N.S. / Kaiser, J.T. / Johnson, E. / Lee, A. / Rees, D.C.
History
DepositionJun 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: D-methionine transport system permease protein metI
B: D-methionine transport system permease protein metI
C: Methionine import ATP-binding protein metN
D: Methionine import ATP-binding protein metN
E: D-methionine transport system permease protein metI
F: D-methionine transport system permease protein metI
G: Methionine import ATP-binding protein metN
H: Methionine import ATP-binding protein metN


Theoretical massNumber of molelcules
Total (without water)244,4058
Polymers244,4058
Non-polymers00
Water0
1
A: D-methionine transport system permease protein metI
B: D-methionine transport system permease protein metI
C: Methionine import ATP-binding protein metN
D: Methionine import ATP-binding protein metN


Theoretical massNumber of molelcules
Total (without water)122,2024
Polymers122,2024
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8920 Å2
ΔGint-58.2 kcal/mol
Surface area52240 Å2
MethodPISA
2
E: D-methionine transport system permease protein metI
F: D-methionine transport system permease protein metI
G: Methionine import ATP-binding protein metN
H: Methionine import ATP-binding protein metN


Theoretical massNumber of molelcules
Total (without water)122,2024
Polymers122,2024
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9960 Å2
ΔGint-60.5 kcal/mol
Surface area52070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.700, 165.400, 289.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsAuthors state that there are two full transporters per asymmetric unit corresponding to chains A,B,C,D and E,F,G,H, respectively.

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Components

#1: Protein
D-methionine transport system permease protein metI


Mass: 23269.947 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: metI, yaeE, b0198, JW0194 / Production host: Escherichia coli (E. coli) / References: UniProt: P31547
#2: Protein
Methionine import ATP-binding protein metN


Mass: 37831.281 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: metN, abc, b0199, JW0195 / Production host: Escherichia coli (E. coli)
References: UniProt: P30750, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 4.78 Å3/Da / Density % sol: 74.25 %

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL11-111
SYNCHROTRONSSRL BL9-221.5
Detector
TypeIDDetector
MARMOSAIC 325 mm CCD1CCD
MARMOSAIC 325 mm CCD2CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.51
ReflectionResolution: 3.7→39.9 Å / Num. obs: 50639

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Processing

Software
NameVersionClassification
CNS1.2refinement
Blu-Icedata collection
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 3.7→39.9 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 16743703.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.347 5070 10 %RANDOM
Rwork0.31 ---
obs0.31 50639 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 104.023 Å2 / ksol: 0.25 e/Å3
Displacement parametersBiso mean: 179.4 Å2
Baniso -1Baniso -2Baniso -3
1--25.03 Å20 Å20 Å2
2--70.35 Å20 Å2
3----45.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.71 Å0.63 Å
Luzzati d res low-5 Å
Luzzati sigma a1.4 Å1.3 Å
Refinement stepCycle: LAST / Resolution: 3.7→39.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16688 0 0 0 16688
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.022
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.14
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.7→3.93 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.474 823 9.8 %
Rwork0.455 7540 -
obs--100 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top

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