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- PDB-6mbn: LptB E163Q in complex with ATP -

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Basic information

Entry
Database: PDB / ID: 6mbn
TitleLptB E163Q in complex with ATP
ComponentsLipopolysaccharide export system ATP-binding protein LptB
KeywordsLIPID TRANSPORT / LptB / lipopolysaccharide / LPS transport / ABC-transporter / ATP-binding cassette
Function / homology
Function and homology information


Translocases; Catalysing the translocation of carbohydrates and their derivatives; Linked to the hydrolysis of a nucleoside triphosphate / transporter complex / lipopolysaccharide transport / Gram-negative-bacterium-type cell outer membrane assembly / ATP-binding cassette (ABC) transporter complex / transmembrane transport / ATP hydrolysis activity / ATP binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Branched-chain amino acid ATP-binding cassette transporter, C-terminal / Branched-chain amino acid ATP-binding cassette transporter / LPS export ABC transporter, ATP-binding protein LptB / 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 / ATPases associated with a variety of cellular activities ...Branched-chain amino acid ATP-binding cassette transporter, C-terminal / Branched-chain amino acid ATP-binding cassette transporter / LPS export ABC transporter, ATP-binding protein LptB / 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 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Lipopolysaccharide export system ATP-binding protein LptB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.957 Å
AuthorsOwens, T.W. / Ruiz, N. / Kahne, D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM066174 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI081059 United States
CitationJournal: Mbio / Year: 2019
Title: Combining Mutations That Inhibit Two Distinct Steps of the ATP Hydrolysis Cycle Restores Wild-Type Function in the Lipopolysaccharide Transporter and Shows that ATP Binding Triggers Transport.
Authors: Simpson, B.W. / Pahil, K.S. / Owens, T.W. / Lundstedt, E.A. / Davis, R.M. / Kahne, D. / Ruiz, N.
History
DepositionAug 30, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lipopolysaccharide export system ATP-binding protein LptB
B: Lipopolysaccharide export system ATP-binding protein LptB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8308
Polymers53,5852
Non-polymers1,2456
Water4,324240
1
A: Lipopolysaccharide export system ATP-binding protein LptB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5075
Polymers26,7931
Non-polymers7144
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lipopolysaccharide export system ATP-binding protein LptB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3233
Polymers26,7931
Non-polymers5302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.351, 137.585, 100.971
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 13 or (resid 14...
21(chain B and (resid 1 through 51 or resid 53...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERTYRTYR(chain A and (resid 1 through 13 or (resid 14...AA1 - 131 - 13
12LYSLYSLYSLYS(chain A and (resid 1 through 13 or (resid 14...AA1414
13SERSERLEULEU(chain A and (resid 1 through 13 or (resid 14...AA1 - 2411 - 241
14SERSERLEULEU(chain A and (resid 1 through 13 or (resid 14...AA1 - 2411 - 241
15SERSERLEULEU(chain A and (resid 1 through 13 or (resid 14...AA1 - 2411 - 241
16SERSERLEULEU(chain A and (resid 1 through 13 or (resid 14...AA1 - 2411 - 241
21SERSERGLYGLY(chain B and (resid 1 through 51 or resid 53...BB1 - 511 - 51
22VALVALALAALA(chain B and (resid 1 through 51 or resid 53...BB53 - 7653 - 76
23ARGARGALAALA(chain B and (resid 1 through 51 or resid 53...BB78 - 1078 - 10
24SERSERLEULEU(chain B and (resid 1 through 51 or resid 53...BB1 - 2411 - 241
25SERSERLEULEU(chain B and (resid 1 through 51 or resid 53...BB1 - 2411 - 241
26SERSERLEULEU(chain B and (resid 1 through 51 or resid 53...BB1 - 2411 - 241
27SERSERLEULEU(chain B and (resid 1 through 51 or resid 53...BB1 - 2411 - 241
28SERSERLEULEU(chain B and (resid 1 through 51 or resid 53...BB1 - 2411 - 241

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Components

#1: Protein Lipopolysaccharide export system ATP-binding protein LptB


Mass: 26792.564 Da / Num. of mol.: 2 / Mutation: E163Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: lptB, yhbG, b3201, JW3168 / Plasmid: pET28b+ / Production host: Escherichia coli KRX (bacteria)
References: UniProt: P0A9V1, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.11 Å3/Da / Density % sol: 41.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 27.5% PEG 4000, 0.6M NaCl, 50mM MES pH = 7.0, 2mM ATP, 1mM EDTA

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.96→100.97 Å / Num. obs: 32858 / % possible obs: 99.2 % / Redundancy: 3.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.068 / Rrim(I) all: 0.133 / Net I/σ(I): 9.4 / Num. measured all: 118625 / Scaling rejects: 19
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.96-2.013.31.476733622060.3810.9251.7510.994.8
8.97-100.973.40.02212763790.9990.0130.02634.195.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.96 Å56.85 Å
Translation1.96 Å56.85 Å

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
XDSdata reduction
Aimless0.5.23data scaling
PHASER2.8.0phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P33

4p33


Resolution: 1.957→56.852 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2187 1570 4.79 %
Rwork0.1873 --
obs0.1888 32755 98.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 157.59 Å2 / Biso mean: 35.9462 Å2 / Biso min: 15.47 Å2
Refinement stepCycle: final / Resolution: 1.957→56.852 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3738 0 116 240 4094
Biso mean--32.36 36.58 -
Num. residues----482
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2124X-RAY DIFFRACTION7.307TORSIONAL
12B2124X-RAY DIFFRACTION7.307TORSIONAL

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