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- PDB-3tuj: Inward facing conformations of the MetNI methionine ABC transport... -

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Basic information

Entry
Database: PDB / ID: 3tuj
TitleInward facing conformations of the MetNI methionine ABC transporter: DM crystal form
Components
  • D-methionine transport system permease protein metI
  • Methionine import ATP-binding protein MetN
KeywordsHYDROLASE/TRANSPORT PROTEIN / ABC-TRANSPORTER / TYPE I ABC TYPE IMPORTER / METHIONINE UPTAKE TRANSPORTER / MEMBRANE PROTEIN / AMINO-ACID TRANSPORT / ATP-BINDING / HYDROLASE / INNER MEMBRANE / HYDROLASE-TRANSPORT PROTEIN 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 / ATPase-coupled transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / 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 / ATPase-coupled transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / 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 / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsJohnson, E. / Nguyen, P. / Rees, D.C.
CitationJournal: Protein Sci. / Year: 2012
Title: Inward facing conformations of the MetNI methionine ABC transporter: Implications for the mechanism of transinhibition.
Authors: Johnson, E. / Nguyen, P.T. / Yeates, T.O. / Rees, D.C.
History
DepositionSep 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Database references

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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


Theoretical massNumber of molelcules
Total (without water)129,4484
Polymers129,4484
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9230 Å2
ΔGint-48 kcal/mol
Surface area50580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.750, 164.130, 212.040
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

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


Mass: 23738.896 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b0198, JW0194, metI, yaeE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21* / References: UniProt: P31547
#2: Protein Methionine import ATP-binding protein MetN


Mass: 40985.348 Da / Num. of mol.: 2 / Mutation: E166Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: abc, b0199, JW0195, metN / Production host: Escherichia coli (E. coli) / Strain (production host): BL21*
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: 1

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Sample preparation

CrystalDensity Matthews: 5.23 Å3/Da / Density % sol: 76.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.5mM TCEP, 0.1M sodium chloride, 0.1M magnesium chloride, 0.1M HEPES, pH 7.5, 33% v/v polyethylene glycol 400, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97901 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 15, 2010
RadiationMonochromator: Liquid nitrogen-cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97901 Å / Relative weight: 1
ReflectionRedundancy: 16.5 % / Av σ(I) over netI: 4.5 / Number: 427428 / Rsym value: 0.11 / D res high: 3.85 Å / D res low: 129.791 Å / Num. obs: 25904 / % possible obs: 99.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
12.1719.8577.210.0430.04314.6
8.6112.1710010.0460.04615.3
7.038.6110010.0610.06115.9
6.097.0310010.1290.12916.4
5.446.0910010.220.2216.6
4.975.4410010.2780.27816.7
4.64.9710010.310.3116.7
4.34.610010.4590.45916.7
4.064.310010.9710.97116.8
3.854.0610012.0512.05116.8
ReflectionResolution: 3.85→129.791 Å / Num. all: 25904 / Num. obs: 25904 / % possible obs: 99.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 16.5 % / Rsym value: 0.11 / Net I/σ(I): 14.3
Reflection shell

Rmerge(I) obs: 0.021 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3.85-4.0616.80.46318137610.02051100
4.06-4.316.80.86015335800.971100
4.3-4.616.71.65600133440.459100
4.6-4.9716.72.45241831330.31100
4.97-5.4416.72.64824928910.278100
5.44-6.0916.63.34348526200.22100
6.09-7.0316.45.53837023360.129100
7.03-8.6115.99.83175119960.061100
8.61-12.1715.312.22378515570.046100
12.17-19.85214.613.6100356860.04377.2

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
XDSdata reduction
PHASEREP/MRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4→19.852 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7853 / SU ML: 1.64 / σ(F): 1.9 / Phase error: 28.21 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2953 1664 7.35 %random
Rwork0.2593 ---
obs0.2618 22647 98.05 %-
all-23097 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 93.535 Å2 / ksol: 0.25 e/Å3
Displacement parametersBiso max: 317.95 Å2 / Biso mean: 190.6678 Å2 / Biso min: 107.69 Å2
Baniso -1Baniso -2Baniso -3
1-5.197 Å2-0 Å2-0 Å2
2---5.0594 Å2-0 Å2
3----0.1376 Å2
Refinement stepCycle: LAST / Resolution: 4→19.852 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8559 0 0 0 8559
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0138705
X-RAY DIFFRACTIONf_angle_d1.28811837
X-RAY DIFFRACTIONf_chiral_restr0.0661447
X-RAY DIFFRACTIONf_plane_restr0.0091497
X-RAY DIFFRACTIONf_dihedral_angle_d12.5533181
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4-4.11670.39131240.3481354147879
4.1167-4.24830.39551510.36011704185598
4.2483-4.39860.32981510.336117531904100
4.3986-4.57260.32921470.289217781925100
4.5726-4.7780.31561230.257117531876100
4.778-5.0260.31291240.254217931917100
5.026-5.33520.31451540.278417711925100
5.3352-5.73790.34231260.292718011927100
5.7379-6.29850.26741540.282817581912100
6.2985-7.1720.31191440.267817961940100
7.172-8.89840.20881250.191518361961100
8.8984-19.85180.27711410.235618862027100

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