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- PDB-6mgf: untagged, wild-type LptB in complex with ADP -

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Basic information

Entry
Database: PDB / ID: 6mgf
Titleuntagged, wild-type LptB in complex with ADP
ComponentsLipopolysaccharide export system ATP-binding protein LptB
KeywordsLIPID TRANSPORT / LptB / lipopolysaccharide / LPS transport / ABC-transporter / ATP-binding cassette / activator
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'-DIPHOSPHATE / Chem-CZJ / Lipopolysaccharide export system ATP-binding protein LptB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.982 Å
AuthorsMandler, M.D. / Owens, 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: not published
Title: Bypassing the requirement for coupling of ATP binding and hydrolysis in the lipopolysaccharide ABC transporte
Authors: Simpson, B. / Ruiz, N.
History
DepositionSep 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / citation / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.name / _citation.journal_abbrev ..._chem_comp.name / _citation.journal_abbrev / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)27,8764
Polymers26,8381
Non-polymers1,0383
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.742, 34.767, 62.897
Angle α, β, γ (deg.)90.000, 100.070, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 26837.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: lptB, yhbG, b3201, JW3168 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0A9V1, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-CZJ / (3s,5s,7s)-N-{7-[(3-O-carbamoyl-6-deoxy-5-methyl-4-O-methyl-beta-D-gulopyranosyl)oxy]-4-hydroxy-8-methyl-2-oxo-2H-1-ben zopyran-3-yl}tricyclo[3.3.1.1~3,7~]decane-1-carboxamide / novobiocin derivative


Mass: 586.630 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H38N2O10
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.07 Å3/Da / Density % sol: 40.6 %
Crystal growTemperature: 296 K / Method: liquid diffusion / pH: 6.5
Details: 22% w/v PEG 4000, 100mM MES pH 6.5, 1.3mM novobiocin-adamantyl, 7% DMSO

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.98→61.93 Å / Num. obs: 4568 / % possible obs: 98.2 % / Redundancy: 5.2 % / Biso Wilson estimate: 40.25 Å2 / CC1/2: 0.967 / Rmerge(I) obs: 0.294 / Rpim(I) all: 0.137 / Rrim(I) all: 0.326 / Net I/σ(I): 6.4 / Num. measured all: 23772 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.98-3.164.41.0936720.5910.5531.23189.4
8.95-61.934.80.0721900.9940.0360.08199.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.31 Å61.93 Å
Translation5.31 Å61.93 Å

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Processing

Software
NameVersionClassification
Aimless0.5.29data scaling
PHASER2.8.1phasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6B8B

6b8b


Resolution: 2.982→61.928 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.71
RfactorNum. reflection% reflection
Rfree0.2367 456 9.99 %
Rwork0.2012 --
obs0.2048 4566 98.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 103.58 Å2 / Biso mean: 42.2853 Å2 / Biso min: 4.97 Å2
Refinement stepCycle: final / Resolution: 2.982→61.928 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1855 0 70 8 1933
Biso mean--61.48 17.12 -
Num. residues----240
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.982-3.41340.30271450.25921303144894
3.4134-4.30040.23631540.193313811535100
4.3004-61.94120.20431570.178714261583100
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)
15.5757-0.6777-0.78894.36631.09984.53690.12170.26680.1388-0.0253-0.03710.5758-0.3809-0.4204-0.2620.2765-0.0476-0.04460.2470.03820.2289-22.1254-15.447711.445
21.5678-1.26990.8081.49830.15053.0977-0.15930.0628-0.28910.31790.01580.20330.0135-0.31460.10880.2229-0.06390.02360.27080.06760.2492-18.9044-14.402914.4117
34.62150.5079-0.48562.47540.80113.44720.2012-0.5666-0.94780.3167-0.4278-0.17970.2658-0.13440.19530.284-0.050.07410.30240.07230.3441-16.6001-25.775519.3733
43.3428-1.6131.99312.1522-0.92295.03210.4228-0.1938-0.3572-0.0593-0.24990.26450.23580.5276-0.18120.3752-0.1262-0.02060.6301-0.06860.41190.0546-20.676127.3085
55.7932-1.44771.55991.5531.32622.9070.48530.3027-0.4934-0.14090.4602-0.84981.22771.8296-0.52970.66810.3088-0.02470.8034-0.25770.88967.9259-27.8523.0562
61.4371-2.13252.68793.676-3.2626.2742-0.41540.44560.39660.21290.0911-0.6408-1.05820.76840.1530.4225-0.1778-0.02380.98680.05440.336110.0243-13.42524.5364
72.04710.9230.59181.8151-1.95974.09020.0650.0053-0.01630.157-0.2063-0.5303-0.19320.7080.17980.2494-0.01410.01120.3727-0.030.4098-0.223-14.822113.6394
83.0345-2.16112.5393.5634-0.43062.99460.1078-0.28720.30260.1023-0.1178-0.385-0.1689-0.0458-0.02930.2889-0.07080.0620.39630.01720.2419-9.4445-11.76124.4626
92.7516-1.4355-1.90811.90230.16433.385-0.08310.3802-0.3913-0.1311-0.21370.26250.0955-0.94840.1440.204-0.0041-0.07580.41320.07030.32-18.4555-9.7921-1.9796
109.85564.4837-8.79712.0429-4.00397.86021.3166-0.42491.22030.879-0.6763-0.2359-1.05860.572-0.0980.65250.1494-0.09750.49730.01830.4458-15.42071.2562-3.6945
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 30 )A2 - 30
2X-RAY DIFFRACTION2chain 'A' and (resid 31 through 62 )A31 - 62
3X-RAY DIFFRACTION3chain 'A' and (resid 63 through 83 )A63 - 83
4X-RAY DIFFRACTION4chain 'A' and (resid 84 through 110 )A84 - 110
5X-RAY DIFFRACTION5chain 'A' and (resid 111 through 124 )A111 - 124
6X-RAY DIFFRACTION6chain 'A' and (resid 125 through 139 )A125 - 139
7X-RAY DIFFRACTION7chain 'A' and (resid 140 through 185 )A140 - 185
8X-RAY DIFFRACTION8chain 'A' and (resid 186 through 211 )A186 - 211
9X-RAY DIFFRACTION9chain 'A' and (resid 212 through 227 )A212 - 227
10X-RAY DIFFRACTION10chain 'A' and (resid 228 through 241 )A228 - 241

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