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- PDB-6cvl: Crystal structure of the Escherichia coli ATPgS-bound MetNI methi... -

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Basic information

Entry
Database: PDB / ID: 6cvl
TitleCrystal structure of the Escherichia coli ATPgS-bound MetNI methionine ABC transporter in complex with its MetQ binding protein
Components
  • MetI transmembrane subunit
  • MetN nucleotide-binding subunit
  • MetQ periplasmic binding protein
KeywordsMEMBRANE PROTEIN / MetNIQ / Outward-facing conformation / Catalytic intermediate state
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 / outer membrane-bounded periplasmic space / 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 / Lipoprotein NlpA family / NlpA lipoprotein / 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 / Lipoprotein NlpA family / NlpA lipoprotein / 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. / Periplasmic binding protein-like II / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / D-Maltodextrin-Binding Protein; domain 2 / Prokaryotic membrane lipoprotein lipid attachment site 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
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / : / IODIDE ION / D-methionine-binding lipoprotein MetQ / 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 / SAD / molecular replacement / Resolution: 2.953 Å
AuthorsNguyen, P.T. / Kaiser, J.T. / Rees, D.C.
Funding support United States, Viet Nam, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
Vietnam International Education DevelopmentViet Nam
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Noncanonical role for the binding protein in substrate uptake by the MetNI methionine ATP Binding Cassette (ABC) transporter.
Authors: Nguyen, P.T. / Lai, J.Y. / Lee, A.T. / Kaiser, J.T. / Rees, D.C.
History
DepositionMar 28, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Advisory / Author supporting evidence / Category: pdbx_audit_support / pdbx_database_PDB_obs_spr / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 27, 2022Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_database_PDB_obs_spr / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: MetN nucleotide-binding subunit
A: MetI transmembrane subunit
B: MetI transmembrane subunit
D: MetN nucleotide-binding subunit
E: MetQ periplasmic binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,44412
Polymers146,5425
Non-polymers1,9027
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18130 Å2
ΔGint-150 kcal/mol
Surface area52270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.960, 107.960, 354.520
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
12(chain C and (resid 0 through 167 or (resid 168...
22(chain D and (resid 0 through 164 or (resid 165...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA1 - 215
211chain BB1 - 215
112(chain C and (resid 0 through 167 or (resid 168...C0 - 167
122(chain C and (resid 0 through 167 or (resid 168...C168
132(chain C and (resid 0 through 167 or (resid 168...C0 - 343
142(chain C and (resid 0 through 167 or (resid 168...C0 - 343
152(chain C and (resid 0 through 167 or (resid 168...C0 - 343
162(chain C and (resid 0 through 167 or (resid 168...C0 - 343
172(chain C and (resid 0 through 167 or (resid 168...C0 - 343
212(chain D and (resid 0 through 164 or (resid 165...D0 - 164
222(chain D and (resid 0 through 164 or (resid 165...D165
232(chain D and (resid 0 through 164 or (resid 165...D0 - 343
242(chain D and (resid 0 through 164 or (resid 165...D0 - 343
252(chain D and (resid 0 through 164 or (resid 165...D0 - 343
262(chain D and (resid 0 through 164 or (resid 165...D0 - 343
272(chain D and (resid 0 through 164 or (resid 165...D0 - 343
282(chain D and (resid 0 through 164 or (resid 165...D0 - 343

NCS ensembles :
ID
1
2

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Components

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Protein , 3 types, 5 molecules CDABE

#1: Protein MetN nucleotide-binding subunit


Mass: 37925.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: metN, abc, b0199, JW0195
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG
References: UniProt: P30750, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances
#2: Protein MetI transmembrane subunit


Mass: 22983.574 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: metI, yaeE, b0198, JW0194 / Production host: Escherichia coli (E. coli) / References: UniProt: P31547
#3: Protein MetQ periplasmic binding protein


Mass: 24724.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: metQ, yaeC, b0197, JW0193
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: P28635

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Non-polymers , 3 types, 7 molecules

#4: Chemical ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Hg
#5: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#6: Chemical ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I

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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: 4.07 Å3/Da / Density % sol: 69.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 22% PEG 400, 0.1M MES pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.00582 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00582 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.33
ReflectionResolution: 2.95→39.853 Å / Num. obs: 43138 / % possible obs: 83.7 % / Redundancy: 19.038 % / CC1/2: 0.999 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.03058 / Rrim(I) all: 0.133 / Χ2: 0.953 / Net I/σ(I): 14.64 / Num. measured all: 821267
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.95-3.0316.5491.8741.45488237482950.4721.9337.9
3.03-3.1117.1891.7761.581502336648740.6461.8323.9
3.11-3.216.4981.7241.5128014354016980.6531.77848
3.2-3.315.5451.8511.3449169344831630.7021.91191.7
3.3-3.4118.6991.5292.0162662335733510.8621.57299.8
3.41-3.5320.0550.9953.1565581327132700.9641.021100
3.53-3.6620.8530.714.5665083312231210.9660.728100
3.66-3.8120.6930.4597.0663009304530450.980.47100
3.81-3.9820.2380.3259.459156292329230.9910.333100
3.98-4.1819.3490.23613.1853790278127800.9940.242100
4.18-4.419.3270.15518.350715262626240.9970.1699.9
4.4-4.6720.3690.13322.1752043255625550.9970.137100
4.67-4.9920.060.11724.7647462236623660.9980.121100
4.99-5.3919.4080.12124.5343570224522450.9980.124100
5.39-5.9118.5730.1225.3137889204220400.9960.12399.9
5.91-6.619.8350.10529.2637032186718670.9980.108100
6.6-7.6218.5370.08534.2131180168216820.9970.087100
7.62-9.3417.0610.06937.4324448143614330.9980.07199.8
9.34-13.2117.9330.06640.1120444114011400.9970.068100
13.21-39.85315.1880.06436.69101157076660.9980.06694.2

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Phasing

Phasing
Method
SAD
molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
DMphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.953→39.853 Å / Cross valid method: THROUGHOUT / σ(F): 1.89 / Phase error: 32.39 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2262 2174 5.07 %
Rwork0.2082 40764 -
obs0.2111 42969 83.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 273.43 Å2 / Biso mean: 113.9151 Å2 / Biso min: 53.43 Å2
Refinement stepCycle: final / Resolution: 2.953→39.853 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10291 0 94 0 10385
Biso mean--74.71 --
Num. residues----1344
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1988X-RAY DIFFRACTION5.273TORSIONAL
12B1988X-RAY DIFFRACTION5.273TORSIONAL
21C3343X-RAY DIFFRACTION5.273TORSIONAL
22D3343X-RAY DIFFRACTION5.273TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9754-3.040.431190.385331833710
3.04-3.11070.3438400.311771275223
3.1107-3.18850.3338690.28281303137242
3.1885-3.27470.31391250.29422458258379
3.2747-3.3710.28341540.2692934308895
3.371-3.47970.26381560.2532950310695
3.4797-3.6040.27121500.24872958310895
3.604-3.74820.24511380.24262959309796
3.7482-3.91860.23251660.22632928309495
3.9186-4.1250.21431580.21412985314395
4.125-4.38310.20461620.19292935309795
4.3831-4.72110.20331490.18693022317195
4.7211-5.19520.19821840.19392998318294
5.1952-5.94470.23471680.23073012318095
5.9447-7.48140.23831840.22563042322694
7.4814-39.39450.20251520.17023250340296
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2121-0.2405-0.46750.3880.70251.08240.5656-0.10660.43990.23120.2554-0.29630.11670.59620.10231.2546-0.1141-0.03311.57960.07541.261115.1999-37.585273.9205
20.981.2551-0.01871.5948-0.25431.03010.5785-2.02540.64981.1642-0.5854-0.166-0.67550.0818-0.04011.1405-0.4611-0.04762.1898-0.21341.002415.4082-40.912983.5264
30.25050.0003-0.09090.09780.09170.11620.63061.40050.1444-0.21540.18920.48680.59041.4620.13062.3722-0.70020.16372.1745-0.43861.441422.3306-72.6715-27.4522
40.81150.0551-0.36390.2625-0.08350.2131-0.1738-0.3029-0.3864-0.60071.2182-1.09240.23440.06880.2361.6706-0.41230.22252.2148-0.21571.097132.0124-69.525-21.8727
51.91010.70781.22684.020.981.116-1.0577-0.3018-0.16010.33910.48970.73430.0178-0.0423-0.22012.0718-0.84440.31032.8315-0.16761.063936.9026-61.6036-29.7267
63.74062.34092.00952.01983.14597.8729-0.19580.79811.5658-1.25110.52841.3082-1.6783-1.0116-1.91231.7918-0.84320.19431.77480.39231.217917.4293-40.7603-31.2743
71.2635-0.61540.64170.5323-0.39960.35370.35370.0786-0.3039-0.4558-0.8796-0.05730.2066-0.70780.053.93021.13110.81452.83930.56771.612728.8536-47.0653-32.102
81.01421.88070.14154.05821.25991.557-0.18740.33120.6861-1.1284-0.25070.6368-0.0056-0.3423-0.54632.0142-0.6435-0.0541.43910.09451.039525.9458-41.546-27.2556
95.2354-0.0960.59751.5915-0.26130.9507-1.27780.64051.09610.04211.2103-0.1271-0.388-0.2652-0.17821.4973-0.64630.42161.7283-0.22451.120124.2679-57.1669-33.6832
102.5263-0.96921.61111.9007-1.671.9549-0.25440.14450.3712-0.2265-0.53690.230.90151.3811-0.51322.6343-0.38190.72072.0611-0.62521.660725.8614-75.1568-35.7155
112.73370.0216-0.71281.593-1.85084.6135-0.1894-0.07820.2177-0.1980.29610.2104-0.256-1.1014-0.01390.51360.0094-0.0081.0494-0.03850.65173.3473-45.73944.1461
120.50640.951-0.50482.2204-1.24141.32070.2596-0.5713-0.61750.997-0.2310.27720.02-0.0781-0.01670.83510.07840.03721.54140.20030.761711.0278-58.824979.6989
130.5254-0.6720.64512.0940.4251.8648-0.04420.02080.18140.05830.0530.6377-0.0957-0.5046-2.41870.5996-0.1919-0.17770.56610.02580.421915.0477-46.97062.9926
142.1308-0.989-0.08110.84481.25192.907-0.0540.28080.1213-0.18320.176-0.0259-0.294-0.25350.00010.74-0.25290.02780.65420.04290.693320.2222-46.68083.7788
150.45310.593-0.50530.7785-0.6290.5127-0.11930.3884-0.1778-0.4896-0.1051-0.22341.05980.081-0.44371.0573-0.17880.15670.8709-0.17660.754122.0057-69.52010.2554
160.3085-0.4271-0.00050.66980.0850.08060.1127-0.65940.39091.0761-0.477-0.2256-0.40530.36390.0010.9203-0.3130.08231.1988-0.06410.96238.1515-52.498515.1464
171.3702-0.20390.321.3244-0.00790.803-0.18210.35070.0479-0.5050.5491-0.23460.27710.64220.00820.8837-0.23630.10820.923-0.06070.672931.5549-61.51696.778
180.73930.3930.24810.6624-0.19520.2638-0.33870.71430.0125-0.36470.16290.25520.62490.12880.02760.9534-0.22310.11860.7657-0.16170.748524.7923-63.667912.9544
191.2994-0.4298-0.05811.001-0.56760.47470.37320.3722-0.5725-0.61870.3733-0.0873-0.9797-0.29260.1470.9831-0.25310.06460.8972-0.11340.879610.2794-65.2199-2.8434
203.70391.30970.24052.33170.39813.45320.0454-0.0469-0.27810.0467-0.3374-0.37230.2810.3665-0.00070.5615-0.04870.02340.77660.09080.680929.7752-57.547248.2811
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'D' and (resid 230 through 282 )D230 - 282
2X-RAY DIFFRACTION2chain 'D' and (resid 283 through 343 )D283 - 343
3X-RAY DIFFRACTION3chain 'E' and (resid 34 through 56 )E34 - 56
4X-RAY DIFFRACTION4chain 'E' and (resid 57 through 88 )E57 - 88
5X-RAY DIFFRACTION5chain 'E' and (resid 89 through 113 )E89 - 113
6X-RAY DIFFRACTION6chain 'E' and (resid 114 through 138 )E114 - 138
7X-RAY DIFFRACTION7chain 'E' and (resid 139 through 151 )E139 - 151
8X-RAY DIFFRACTION8chain 'E' and (resid 152 through 195 )E152 - 195
9X-RAY DIFFRACTION9chain 'E' and (resid 196 through 240 )E196 - 240
10X-RAY DIFFRACTION10chain 'E' and (resid 241 through 259 )E241 - 259
11X-RAY DIFFRACTION11chain 'C' and (resid 0 through 229 )C0 - 229
12X-RAY DIFFRACTION12chain 'C' and (resid 230 through 343 )C230 - 343
13X-RAY DIFFRACTION13chain 'A' and (resid 1 through 65 )A1 - 65
14X-RAY DIFFRACTION14chain 'A' and (resid 66 through 215 )A66 - 215
15X-RAY DIFFRACTION15chain 'B' and (resid 1 through 40 )B1 - 40
16X-RAY DIFFRACTION16chain 'B' and (resid 41 through 65 )B41 - 65
17X-RAY DIFFRACTION17chain 'B' and (resid 66 through 126 )B66 - 126
18X-RAY DIFFRACTION18chain 'B' and (resid 127 through 170 )B127 - 170
19X-RAY DIFFRACTION19chain 'B' and (resid 171 through 215 )B171 - 215
20X-RAY DIFFRACTION20chain 'D' and (resid 0 through 229 )D0 - 229

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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