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

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Basic information

Entry
Database: PDB / ID: 3tui
TitleInward facing conformations of the MetNI methionine ABC transporter: CY5 native 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 / 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: 2.9 Å
AuthorsJohnson, E. / Nguyen, P.T. / 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
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

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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)257,22912
Polymers255,5218
Non-polymers1,7094
Water2,630146
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)128,6156
Polymers127,7604
Non-polymers8542
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10030 Å2
ΔGint-57 kcal/mol
Surface area49320 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)128,6156
Polymers127,7604
Non-polymers8542
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9920 Å2
ΔGint-56 kcal/mol
Surface area49280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.430, 140.080, 150.070
Angle α, β, γ (deg.)90.00, 96.39, 90.00
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-ADP / ADENOSINE-5'-DIPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 146 / 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: 3.42 Å3/Da / Density % sol: 64.07 %
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: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 2, 2009
RadiationMonochromator: Liquid nitrogen-cooled double crystal. / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 3.3 % / Av σ(I) over netI: 12.4 / Number: 303926 / Rsym value: 0.041 / D res high: 2.7 Å / D res low: 29.608 Å / Num. obs: 91606 / % possible obs: 97.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
8.5429.6196.210.0180.0184.1
6.048.5499.810.0250.0254.2
4.936.0499.910.0340.0344.2
4.274.9310010.0340.0344.2
3.824.2710010.0590.0594.3
3.493.8210010.120.124.2
3.233.4999.410.2080.2083.6
3.023.2398.210.2090.2092.2
2.853.0298.310.3010.3012.2
2.72.8586.510.4040.4042.1
ReflectionResolution: 2.7→29.608 Å / Num. all: 91606 / Num. obs: 91606 / % possible obs: 97.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rsym value: 0.041 / Net I/σ(I): 12.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.7-2.852.10.4041.90.404186.5
2.85-3.022.20.3012.60.301198.3
3.02-3.232.20.2093.70.209198.2
3.23-3.493.60.2083.70.208199.4
3.49-3.824.20.126.30.121100
3.82-4.274.30.05911.20.0591100
4.27-4.934.20.03414.80.0341100
4.93-6.044.20.03417.40.034199.9
6.04-8.544.20.02520.30.025199.8
8.54-29.6084.10.01830.20.018196.2

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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: 2.9→29.609 Å / Occupancy max: 1 / Occupancy min: 0.89 / SU ML: 1.09 / σ(F): 0 / Phase error: 34.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3029 3692 4.97 %
Rwork0.2404 --
obs0.2435 74334 97.93 %
all-75904 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.985 Å2 / ksol: 0.275 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.5273 Å2-0 Å2-8.2073 Å2
2--2.3742 Å20 Å2
3---0.8602 Å2
Refinement stepCycle: LAST / Resolution: 2.9→29.609 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17132 0 108 146 17386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117537
X-RAY DIFFRACTIONf_angle_d1.46923863
X-RAY DIFFRACTIONf_dihedral_angle_d15.8936421
X-RAY DIFFRACTIONf_chiral_restr0.0882910
X-RAY DIFFRACTIONf_plane_restr0.0072999
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.93820.41221140.4422122X-RAY DIFFRACTION78
2.9382-2.97840.46421080.40682364X-RAY DIFFRACTION84
2.9784-3.02090.43331370.38562486X-RAY DIFFRACTION91
3.0209-3.06590.40461540.3722651X-RAY DIFFRACTION97
3.0659-3.11380.36311580.34862785X-RAY DIFFRACTION100
3.1138-3.16480.3681530.32782712X-RAY DIFFRACTION100
3.1648-3.21930.34081390.30842794X-RAY DIFFRACTION100
3.2193-3.27770.37981210.29982748X-RAY DIFFRACTION100
3.2777-3.34070.34131240.28912841X-RAY DIFFRACTION100
3.3407-3.40880.37721450.26692740X-RAY DIFFRACTION100
3.4088-3.48280.32711590.24582777X-RAY DIFFRACTION100
3.4828-3.56370.30421380.23992736X-RAY DIFFRACTION100
3.5637-3.65270.31371190.23012818X-RAY DIFFRACTION100
3.6527-3.75120.3141490.21972731X-RAY DIFFRACTION100
3.7512-3.86140.31791630.21232761X-RAY DIFFRACTION100
3.8614-3.98570.26791370.20722801X-RAY DIFFRACTION100
3.9857-4.12780.23651530.20642726X-RAY DIFFRACTION100
4.1278-4.29260.25171450.18772803X-RAY DIFFRACTION100
4.2926-4.48740.25251570.1762747X-RAY DIFFRACTION100
4.4874-4.72310.23341410.18382765X-RAY DIFFRACTION100
4.7231-5.01760.32471520.20812774X-RAY DIFFRACTION100
5.0176-5.40290.3171390.22392797X-RAY DIFFRACTION100
5.4029-5.94260.29221500.24672770X-RAY DIFFRACTION100
5.9426-6.79350.3081420.2352797X-RAY DIFFRACTION100
6.7935-8.52510.23951310.19222819X-RAY DIFFRACTION100
8.5251-29.61010.26761640.21812777X-RAY DIFFRACTION98

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