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- PDB-6b89: E. coli LptB in complex with ADP and novobiocin -

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Basic information

Entry
Database: PDB / ID: 6b89
TitleE. coli LptB in complex with ADP and novobiocin
ComponentsLipopolysaccharide export system ATP-binding protein LptB
Keywordslipid transport/activator / LptB / ABC transporter / LPS transport / LIPID TRANSPORT / activator / 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 ...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 / NOVOBIOCIN / 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 Å
AuthorsMay, J.M. / Lazarus, M.B. / Sherman, D.J. / Owens, T.W. / Mandler, M.D. / 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 5, 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 / struct_conn
Item: _audit_author.name / _struct_conn.pdbx_dist_value ..._audit_author.name / _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
Revision 1.4Jan 20, 2021Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.5Oct 4, 2023Group: 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
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
B: Lipopolysaccharide export system ATP-binding protein LptB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0108
Polymers55,8822
Non-polymers2,1286
Water1,820101
1
A: Lipopolysaccharide export system ATP-binding protein LptB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0054
Polymers27,9411
Non-polymers1,0643
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)29,0054
Polymers27,9411
Non-polymers1,0643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)190.319, 35.100, 63.050
Angle α, β, γ (deg.)90.000, 91.520, 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: 27940.760 Da / Num. of mol.: 2
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-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NOV / NOVOBIOCIN / 4-Hydroxy-3-[4-hydroxy-3-(3-methylbut-2-enyl)benzamido]-8-methylcoumarin-7-yl 3-O-carbamoyl-5,5-di-C-methyl-alpha-l-lyxofuranoside


Mass: 612.624 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H36N2O11 / Comment: antibiotic*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.03 Å3/Da / Density % sol: 34.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 100mM MES pH = 6.5, 30% PEG4000

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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: Jun 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2→63.03 Å / Num. obs: 28485 / % possible obs: 99.4 % / Redundancy: 3.5 % / Biso Wilson estimate: 16.33 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.08 / Rrim(I) all: 0.151 / Net I/σ(I): 8.7 / Num. measured all: 99157 / Scaling rejects: 16
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
2-2.053.50.6220.6060.3850.73499.2
8.94-63.033.30.0250.9990.0170.0399

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata collection
Aimless0.5.15data scaling
PHASERphasing
PHENIX1.10_2155refinement
PDB_EXTRACT3.22data extraction
Aimlessdata reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P32

4p32


Resolution: 2→63.028 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 21.19
RfactorNum. reflection% reflectionSelection details
Rfree0.2203 1422 4.99 %random selection
Rwork0.1794 ---
obs0.1815 28479 99.07 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 83.01 Å2 / Biso mean: 20.6277 Å2 / Biso min: 6.08 Å2
Refinement stepCycle: final / Resolution: 2→63.028 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3577 0 216 101 3894
Biso mean--21.34 17.76 -
Num. residues----460
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073824
X-RAY DIFFRACTIONf_angle_d0.7475191
X-RAY DIFFRACTIONf_chiral_restr0.047597
X-RAY DIFFRACTIONf_plane_restr0.004667
X-RAY DIFFRACTIONf_dihedral_angle_d14.3782277
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10 / % reflection obs: 99 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2-2.07150.29671200.24127042824
2.0715-2.15440.281240.218226552779
2.1544-2.25250.27211270.209227102837
2.2525-2.37130.24671460.198726592805
2.3713-2.51980.21421420.1926922834
2.5198-2.71440.24791420.190627002842
2.7144-2.98760.24751470.189426882835
2.9876-3.41980.20931340.173127312865
3.4198-4.30850.18071530.139627162869
4.3085-63.05910.18381870.154828022989
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)
13.0384-3.2874-0.80665.78582.11480.94490.04210.2536-0.38140.1533-0.45980.48650.143-0.34210.38430.1193-0.0139-0.01570.1654-0.03750.1278-44.887-5.91213.844
27.5938-4.7433-2.03985.23451.95823.41080.5758-0.03930.45730.1408-0.39260.50960.0147-0.7878-0.01990.1574-0.04430.06590.1882-0.03270.237-49.3857.66319.947
31.2496-0.8022-0.90281.5506-0.21651.6443-0.0318-0.0371-0.03160.050.0510.06470.0153-0.0468-0.03560.0739-0.0027-0.03170.112-0.02770.12-40.511-2.56213.652
43.84061.18670.4572.43180.64813.91610.1138-0.32-0.10630.2471-0.1523-0.14070.2521-0.1980.02280.10970.0052-0.03840.1188-0.01870.1182-35.768-9.27220.913
57.1744-1.06520.70733.3107-1.62394.8834-0.0227-0.55040.1360.3441-0.2294-0.0543-0.4697-0.26470.08820.06-0.0503-0.0190.12310.0250.0659-17.6061.16527.108
62.23980.0504-1.6137.01770.09663.5692-0.17250.1145-0.49630.38640.229-0.10770.8147-0.0997-0.07340.2329-0.0318-0.04920.1378-0.01640.1891-15.943-13.57123.283
76.29174.32563.87867.43924.59773.3949-0.16890.4418-0.3485-0.50250.4333-0.18010.00520.5459-0.23050.1351-0.01110.00890.1363-0.00470.1131-9.956-3.04417.12
85.24262.65660.44636.676-0.12093.29940.07020.07170.1953-0.0671-0.20670.2138-0.1662-0.01120.10140.08420.01140.00250.0717-0.00050.0406-18.9480.27419.065
94.68712.1273-2.35946.9736-0.37044.2570.11510.01450.0437-0.3955-0.1006-0.2637-0.23980.4263-0.01760.09960.0182-0.03580.1948-0.01660.0926-23.5931.5998.814
106.1862-3.85460.57192.5777-0.13111.68430.23580.34730.1211-0.2724-0.3266-0.4238-0.13920.18840.04310.14320.00550.0140.17480.01650.0993-29.596-1.4956.649
113.762-1.48030.07594.19792.67066.01740.06610.35890.1284-0.0312-0.1906-0.0237-0.04520.05350.08820.0901-0.0083-0.01910.08560.03640.0735-38.8123.5392.495
127.0475-2.62472.36488.6546-2.55771.2454-0.20810.320.36040.09760.0746-0.0956-0.1580.23150.09780.19130.0547-0.04210.23580.04210.1241-43.6639.633-3.295
133.5080.812-1.23363.2086-0.92232.9646-0.0840.0581-0.0486-0.02430.0169-0.1502-0.11020.05490.05660.06910.0079-0.01740.0934-0.0130.0837-7.680.91345.43
144.3745-1.3441.13480.4384-0.1361.47680.05290.0867-0.3282-0.09630.00970.08740.19290.1844-0.07290.15250.00060.01520.0842-0.00580.1136-13.177-7.18839.481
154.1269-1.0463-1.15744.2418-0.82865.2585-0.060.17020.4195-0.2825-0.29610.2557-0.030.32620.28910.07740.0082-0.07140.14380.02440.2276-34.1610.64230.481
163.21-2.38671.2278.9146-1.31636.24860.0793-0.1143-0.6771-0.4878-0.1024-0.47210.84880.0516-0.01030.1793-0.00890.01860.11940.02070.2756-29.49-11.54834.208
178.8962-0.3704-0.79312.324.30778.66360.0141-0.878-0.92080.5915-0.01460.08311.0264-0.11420.00460.2575-0.0440.00350.28670.07340.2542-36.388-11.78841.114
184.91941.5369-1.73623.03780.02965.37610.2068-0.45140.8038-0.10620.08120.5041-0.2033-0.4797-0.17450.11510.0187-0.07290.2611-0.11310.3313-39.3191.94236.209
192.80140.7220.47760.37680.6411.35570.0642-0.29670.2837-0.0978-0.24010.10140.055-0.19490.12610.12650.02530.02130.1506-0.04140.1174-25.953-1.29543.227
206.7794-2.17181.17993.1256-0.97813.21710.0880.20120.67730.50940.27170.2106-0.4067-0.5317-0.34230.18980.08580.05880.25790.0730.186-30.2255.18251.854
212.68473.40880.00385.7245-1.25551.5190.2883-0.28550.43910.4772-0.2940.8085-0.0667-0.3881-0.00180.19760.05520.05830.2926-0.03380.2023-22.195-2.27253.146
223.43061.0497-1.78824.4762-1.54654.46220.0668-0.6970.25450.4982-0.2544-0.0872-0.42670.15290.1650.16820.0305-0.0120.2375-0.06980.1288-11.5875.11156.691
232.2929-2.0255-1.25875.4233-1.74672.94440.1622-1.27170.31371.22680.1958-0.5442-0.31540.3422-0.2670.3137-0.1026-0.0220.5869-0.04890.1568-11.1613.7665.598
249.7128-0.2828224.792921.38985.33162.023-1.066-0.2208-2.4078-0.9625-3.3864-1.15860.4190.22570.05031.5859-0.04150.6389-5.679.01464.744
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:12 )A2 - 12
2X-RAY DIFFRACTION2( CHAIN A AND RESID 13:20 )A13 - 20
3X-RAY DIFFRACTION3( CHAIN A AND RESID 21:63 )A21 - 63
4X-RAY DIFFRACTION4( CHAIN A AND RESID 64:86 )A64 - 86
5X-RAY DIFFRACTION5( CHAIN A AND RESID 87:96 )A87 - 96
6X-RAY DIFFRACTION6( CHAIN A AND RESID 97:122 )A97 - 122
7X-RAY DIFFRACTION7( CHAIN A AND RESID 123:133 )A123 - 133
8X-RAY DIFFRACTION8( CHAIN A AND RESID 134:156 )A134 - 156
9X-RAY DIFFRACTION9( CHAIN A AND RESID 157:182 )A157 - 182
10X-RAY DIFFRACTION10( CHAIN A AND RESID 183:197 )A183 - 197
11X-RAY DIFFRACTION11( CHAIN A AND RESID 198:221 )A198 - 221
12X-RAY DIFFRACTION12( CHAIN A AND RESID 222:235 )A222 - 235
13X-RAY DIFFRACTION13( CHAIN B AND RESID 2:55 )B2 - 55
14X-RAY DIFFRACTION14( CHAIN B AND RESID 56:90 )B56 - 90
15X-RAY DIFFRACTION15( CHAIN B AND RESID 91:96 )B91 - 96
16X-RAY DIFFRACTION16( CHAIN B AND RESID 97:108 )B97 - 108
17X-RAY DIFFRACTION17( CHAIN B AND RESID 109:126 )B109 - 126
18X-RAY DIFFRACTION18( CHAIN B AND RESID 127:138 )B127 - 138
19X-RAY DIFFRACTION19( CHAIN B AND RESID 139:164 )B139 - 164
20X-RAY DIFFRACTION20( CHAIN B AND RESID 165:180 )B165 - 180
21X-RAY DIFFRACTION21( CHAIN B AND RESID 181:196 )B181 - 196
22X-RAY DIFFRACTION22( CHAIN B AND RESID 197:218 )B197 - 218
23X-RAY DIFFRACTION23( CHAIN B AND RESID 219:226 )B219 - 226
24X-RAY DIFFRACTION24( CHAIN B AND RESID 227:227 )B227

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