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

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Basic information

Entry
Database: PDB / ID: 3tuz
TitleInward facing conformations of the MetNI methionine ABC transporter: CY5 SeMet soak 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


methionine-importing ABC transporter complex / methionine import across plasma membrane / ABC-type methionine transporter / ABC-type D-methionine transporter activity / L-methionine transmembrane transporter activity / D-methionine transmembrane transport / methionine transport / Gram-negative-bacterium-type cell wall / ATPase-coupled transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing ...methionine-importing ABC transporter complex / methionine import across plasma membrane / ABC-type methionine transporter / ABC-type D-methionine transporter activity / L-methionine transmembrane transporter activity / D-methionine transmembrane transport / methionine transport / Gram-negative-bacterium-type cell wall / ATPase-coupled transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / 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, 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 / ACT domain / 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-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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / SELENOMETHIONINE / 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: 3.4 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 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Database references
Revision 1.2Sep 13, 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
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)258,01416
Polymers255,5218
Non-polymers2,4938
Water00
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,0078
Polymers127,7604
Non-polymers1,2474
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10210 Å2
ΔGint-63 kcal/mol
Surface area49920 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,0078
Polymers127,7604
Non-polymers1,2474
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10070 Å2
ΔGint-59 kcal/mol
Surface area49550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.310, 138.890, 147.510
Angle α, β, γ (deg.)90.000, 95.720, 90.000
Int Tables number4
Space group name H-MP1211

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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: 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: 40610.191 Da / Num. of mol.: 4 / 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
#3: Chemical
ChemComp-MSE / SELENOMETHIONINE


Type: L-peptide linking / Mass: 196.106 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H11NO2Se
#4: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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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: 3.33 Å3/Da / Density % sol: 63.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% v/v polyethylene glycol 400, 0.1 M tris, pH 7.5, 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: 0.9801 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2010
RadiationMonochromator: Liquid nitrogen-cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionRedundancy: 10.3 % / Av σ(I) over netI: 6.4 / Number: 492148 / Rsym value: 0.076 / D res high: 3.195 Å / D res low: 146.772 Å / Num. obs: 47870 / % possible obs: 86.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
3.193.3749.510.6860.6866.7
10.139.4696.410.0310.03110.5
7.1410.199.210.0370.03711.2
5.837.1499.310.0710.07111.6
5.055.839910.090.0911.2
4.525.0599.210.090.0911.7
4.124.5298.710.1190.11911.3
3.824.1299.310.2380.23811.8
3.573.8288.610.3190.3198.9
3.373.5769.610.4490.4497.5
ReflectionResolution: 3.195→146.772 Å / Num. all: 47870 / Num. obs: 47870 / % possible obs: 86.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 10.3 % / Rsym value: 0.076 / Net I/σ(I): 15.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3.19-3.376.70.6861.12670839800.68649.5
3.37-3.577.50.4491.73957053080.44969.6
3.57-3.828.90.3192.45654663380.31988.6
3.82-4.1211.80.2383.27805166340.23899.3
4.12-4.5211.30.1194.96897960920.11998.7
4.52-5.0511.70.097.46501655340.0999.2
5.05-5.8311.20.0935475848680.0999
5.83-7.1411.60.0719.74809541490.07199.3
7.14-10.111.20.03715.83611632250.03799.2
10.1-39.46310.50.031181830917420.03196.4

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DHW

3dhw


Resolution: 3.4→38.799 Å / Occupancy max: 1 / Occupancy min: 0.56 / FOM work R set: 0.7524 / SU ML: 1.26 / σ(F): 0 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.3055 2156 5.01 %random
Rwork0.2602 ---
all0.2625 43016 --
obs0.2625 43016 93.4 %-
Solvent computationShrinkage radii: 0.27 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.005 Å2 / ksol: 0.288 e/Å3
Displacement parametersBiso max: 213.88 Å2 / Biso mean: 80.7078 Å2 / Biso min: 26.17 Å2
Baniso -1Baniso -2Baniso -3
1--1.9078 Å2-0 Å2-5.4699 Å2
2--2.953 Å20 Å2
3----1.0452 Å2
Refinement stepCycle: LAST / Resolution: 3.4→38.799 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17090 0 144 0 17234
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01217527
X-RAY DIFFRACTIONf_angle_d1.42123844
X-RAY DIFFRACTIONf_chiral_restr0.0852908
X-RAY DIFFRACTIONf_plane_restr0.0082997
X-RAY DIFFRACTIONf_dihedral_angle_d15.416422
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4001-3.47910.44971060.44751962206867
3.4791-3.56610.4231140.37942148226274
3.5661-3.66240.38521230.33872388251182
3.6624-3.77010.34131300.30072654278491
3.7701-3.89170.30121330.27742835296898
3.8917-4.03070.33471560.26792888304499
4.0307-4.19190.30461640.25322860302499
4.1919-4.38240.27591520.22312907305999
4.3824-4.61310.2791550.22112871302699
4.6131-4.90160.27561380.23192896303499
4.9016-5.27920.33131580.26442847300599
5.2792-5.80890.33811370.27362902303999
5.8089-6.64580.32811670.26252887305499
6.6458-8.35920.25811580.19752912307099
8.3592-38.80180.2431650.22542903306898

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