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- PDB-6b8b: E. coli LptB in complex with ADP and a novobiocin derivative -

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Basic information

Entry
Database: PDB / ID: 6b8b
TitleE. coli LptB in complex with ADP and a novobiocin derivative
ComponentsLipopolysaccharide export system ATP-binding protein LptB
Keywordslipid transport/activator / LptB / ABC transporter / LPS transport / LIPID TRANSPORT / lipid transport-activator complex
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: 1.95 Å
AuthorsMandler, M.D. / Owens, T.W. / Lazarus, M.B. / May, J.M. / Kahne, D.K.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM066174 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)AI109764 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)AI081059 United States
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: The Antibiotic Novobiocin Binds and Activates the ATPase That Powers Lipopolysaccharide Transport.
Authors: May, J.M. / Owens, T.W. / Mandler, M.D. / Simpson, B.W. / Lazarus, M.B. / Sherman, D.J. / Davis, R.M. / Okuda, S. / Massefski, W. / Ruiz, N. / Kahne, D.
History
DepositionOct 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 6, 2021Group: Derived calculations / Structure summary
Category: audit_author / chem_comp ...audit_author / chem_comp / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn
Item: _audit_author.name / _chem_comp.name ..._audit_author.name / _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.4Oct 4, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9794
Polymers27,9411
Non-polymers1,0383
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.030, 34.780, 62.710
Angle α, β, γ (deg.)90.000, 101.380, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-504-

HOH

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Components

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


Mass: 27940.760 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 KRX (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-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
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.15 Å3/Da / Density % sol: 38.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100mM MES pH = 6.5, 30% w/v PEG4000, 1.3mM novobiocin-adamantyl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.87→61.48 Å / Num. obs: 52602 / % possible obs: 98.7 % / Redundancy: 2.9 % / Biso Wilson estimate: 24.27 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.063 / Rrim(I) all: 0.11 / Net I/σ(I): 10.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
1.95-22.60.6750.5240.50.84398.6
8.94-43.712.80.0340.9970.0240.04296

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata collection
Aimless0.5.27data scaling
PHASERphasing
PHENIX1.11_2567refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P32

4p32


Resolution: 1.95→43.715 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.24
RfactorNum. reflection% reflectionSelection details
Rfree0.2237 1528 5.06 %Random Selection
Rwork0.18 ---
obs0.1822 30170 96.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 158.1 Å2 / Biso mean: 38.1118 Å2 / Biso min: 11.17 Å2
Refinement stepCycle: final / Resolution: 1.95→43.715 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1817 0 120 105 2042
Biso mean--50.4 37.1 -
Num. residues----233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041942
X-RAY DIFFRACTIONf_angle_d0.9122651
X-RAY DIFFRACTIONf_chiral_restr0.179309
X-RAY DIFFRACTIONf_plane_restr0.003337
X-RAY DIFFRACTIONf_dihedral_angle_d17.011163
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-2.0130.27071560.28642482263894
2.013-2.08490.32581580.2492625278397
2.0849-2.16840.27151470.22652672281997
2.1684-2.26710.25911310.2132579271096
2.2671-2.38660.21641250.20452625275096
2.3866-2.53610.26951550.18762593274896
2.5361-2.73190.23871220.18212656277897
2.7319-3.00680.22051450.17752617276297
3.0068-3.44170.20871410.16042617275896
3.4417-4.33560.18151260.14462581270795
4.3356-43.72590.19681220.16362595271795
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)
10.07120.0965-0.15890.1091-0.08010.09950.22070.0504-0.1388-0.1519-0.1992-0.0128-0.1062-0.2627-0.00160.17620.00210.00110.162-0.0260.233-22.2327-1.383610.0977
20.0363-0.044-0.04390.0170.00120.0315-0.05290.1430.89070.05820.02690.86710.1354-0.3298-0.00010.23770.07210.05680.2875-0.06710.4436-28.84112.345116.7182
30.6065-0.02450.24020.1372-0.16750.4740.07350.0016-0.0053-0.0158-0.07730.0771-0.1049-0.0531-0.00010.1427-0.013-0.00470.1095-0.01280.1679-17.23024.238211.5288
40.1752-0.0158-0.09930.15260.03120.2418-0.0053-0.1581-0.15450.2666-0.12630.28420.3555-0.21670.00210.2115-0.0440.03830.1546-0.00360.2293-21.4225-6.706517.0641
50.22580.1722-0.18910.17110.15040.07520.1252-0.4020.0252-0.0215-0.22410.08210.11990.13460.00010.2612-0.0339-0.00320.189-0.01420.1389-9.11181.570620.6224
60.0757-0.24010.37950.1401-0.27490.3780.10690.1202-0.11370.1822-0.10540.091-0.02030.204300.2495-0.0056-0.00470.3111-0.0270.18150.6981-2.568329.0205
71.58820.69220.65170.8291-0.17021.28140.08450.7488-0.11890.09020.0887-0.07720.13110.59110.17410.22280.0449-0.01080.4587-0.03510.18535.5915-0.797122.608
80.2704-0.05820.0783-0.0040.01960.23710.0676-0.22690.0334-0.05470.0182-0.0280.05720.085-00.1293-0.02570.02740.1389-0.02580.1647-2.06486.990611.978
90.01770.0830.01480.0082-0.0071-0.00770.0492-0.0725-0.1943-0.0448-0.0935-0.0978-0.04350.0441-00.2117-0.0325-0.0110.16920.01170.27891.0017-1.58646.6173
100.11090.04960.1130.24660.17290.1196-0.1298-0.03970.17150.18980.0806-0.22460.0918-0.06040.00270.1445-0.0107-0.0140.13750.0030.2006-7.74538.48316.3303
110.1673-0.03330.09620.0459-0.03960.38460.06160.28040.0356-0.0819-0.0904-0.0092-0.0576-0.1448-0.00010.14880.01-0.00450.14590.00320.1584-16.10217.63190.0716
120.06760.0472-0.01470.0358-0.07350.05670.29690.27910.0104-0.1335-0.40980.7348-0.02490.1605-00.28360.0638-0.04570.29130.05070.243-17.650916.3589-6.6306
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 2:11)A2 - 11
2X-RAY DIFFRACTION2(chain A and resid 12:20)A12 - 20
3X-RAY DIFFRACTION3(chain A and resid 21:55)A21 - 55
4X-RAY DIFFRACTION4(chain A and resid 56:76)A56 - 76
5X-RAY DIFFRACTION5(chain A and resid 77:89)A77 - 89
6X-RAY DIFFRACTION6(chain A and resid 90:108)A90 - 108
7X-RAY DIFFRACTION7(chain A and resid 109:155)A109 - 155
8X-RAY DIFFRACTION8(chain A and resid 156:177)A156 - 177
9X-RAY DIFFRACTION9(chain A and resid 178:186)A178 - 186
10X-RAY DIFFRACTION10(chain A and resid 187:200)A187 - 200
11X-RAY DIFFRACTION11(chain A and resid 201:225)A201 - 225
12X-RAY DIFFRACTION12(chain A and resid 226:232)A226 - 232

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