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- PDB-6mjp: LptB(E163Q)FGC from Vibrio cholerae -

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Basic information

Entry
Database: PDB / ID: 6mjp
TitleLptB(E163Q)FGC from Vibrio cholerae
Components
  • ABC transporter ATP-binding protein
  • FIG000988: Predicted permease
  • LPS export ABC transporter permease LptG
  • Lipopolysaccharide export system protein LptC
KeywordsLIPID TRANSPORT / lipopolysaccharide transport / ABC-transporter
Function / homology
Function and homology information


lipopolysaccharide transmembrane transporter activity / glycolipid transfer activity / lipopolysaccharide transport / Gram-negative-bacterium-type cell outer membrane assembly / ATP-binding cassette (ABC) transporter complex / transmembrane transport / outer membrane-bounded periplasmic space / ATP hydrolysis activity / ATP binding / metal ion binding ...lipopolysaccharide transmembrane transporter activity / glycolipid transfer activity / lipopolysaccharide transport / Gram-negative-bacterium-type cell outer membrane assembly / ATP-binding cassette (ABC) transporter complex / transmembrane transport / outer membrane-bounded periplasmic space / ATP hydrolysis activity / ATP binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Lipopolysaccharide assembly, LptC-related / Lipopolysaccharide export system protein LptC / : / Lipopolysaccharide-assembly, LptC-related / Permease LptG/LptF-related / LPS export ABC transporter permease LptF / LPS export ABC transporter permease LptG / Lipopolysaccharide export system permease LptF/LptG / Branched-chain amino acid ATP-binding cassette transporter, C-terminal / Branched-chain amino acid ATP-binding cassette transporter ...Lipopolysaccharide assembly, LptC-related / Lipopolysaccharide export system protein LptC / : / Lipopolysaccharide-assembly, LptC-related / Permease LptG/LptF-related / LPS export ABC transporter permease LptF / LPS export ABC transporter permease LptG / Lipopolysaccharide export system permease LptF/LptG / 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
2-(2-ETHOXYETHOXY)ETHANOL / 6-cyclohexylhexyl beta-D-glucopyranoside / CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE / DI(HYDROXYETHYL)ETHER / Lipopolysaccharide export system protein LptC / Lipopolysaccharide export system permease protein LptF / LPS export ABC transporter permease LptG / Lipopolysaccharide export system ATP-binding protein LptB / Lipopolysaccharide export system protein LptC / Lipopolysaccharide export system permease protein LptF / Uncharacterized protein
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsOwens, T.W. / Kahne, D. / Kruse, A.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 GM066174 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI081059 United States
CitationJournal: Nature / Year: 2019
Title: Structural basis of unidirectional export of lipopolysaccharide to the cell surface.
Authors: Owens, T.W. / Taylor, R.J. / Pahil, K.S. / Bertani, B.R. / Ruiz, N. / Kruse, A.C. / Kahne, D.
History
DepositionSep 21, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Apr 10, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ABC transporter ATP-binding protein
B: ABC transporter ATP-binding protein
C: Lipopolysaccharide export system protein LptC
F: FIG000988: Predicted permease
G: LPS export ABC transporter permease LptG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,64824
Polymers156,0005
Non-polymers3,64819
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18080 Å2
ΔGint-146 kcal/mol
Surface area61050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.354, 80.729, 202.992
Angle α, β, γ (deg.)90.000, 112.180, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 4 types, 5 molecules ABCFG

#1: Protein ABC transporter ATP-binding protein / ABC transporter family protein / LPS ABC transporter ATP-binding protein / LPS export ABC ...ABC transporter family protein / LPS ABC transporter ATP-binding protein / LPS export ABC transporter ATP-binding protein / Lipopolysaccharide ABC transporter ATP-binding protein / Lipopolysaccharide ABC transporter / ATP-binding protein LptB / Putative ABC transporter ATP-binding protein / Sugar ABC transporter ATP-binding protein


Mass: 26986.006 Da / Num. of mol.: 2 / Mutation: E163Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: lptB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O30650, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances
#2: Protein Lipopolysaccharide export system protein LptC


Mass: 21871.756 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: lptC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A085S5D1, UniProt: Q9KP51*PLUS
#3: Protein FIG000988: Predicted permease / LPS export ABC transporter permease LptF / Lipopolysaccharide ABC transporter permease / ...LPS export ABC transporter permease LptF / Lipopolysaccharide ABC transporter permease / Lipopolysaccharide export system permease


Mass: 40929.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: lptF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0F0BAF3, UniProt: Q9KP75*PLUS
#4: Protein LPS export ABC transporter permease LptG / Lipopolysaccharide ABC transporter permease


Mass: 39226.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: lptG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H6JG76, UniProt: Q9KP76*PLUS

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Sugars , 1 types, 3 molecules

#11: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 9 types, 69 molecules

#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-AE3 / 2-(2-ETHOXYETHOXY)ETHANOL


Mass: 134.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O3
#8: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#9: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#10: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#12: Chemical ChemComp-JU7 / 6-cyclohexylhexyl beta-D-glucopyranoside


Mass: 346.459 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O6
#13: Chemical ChemComp-MA4 / CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE


Mass: 508.600 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H44O11
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 4.06 Å3/Da / Density % sol: 69.7 %
Description: Long triangular plates growing in radial clusters.
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 41% PEG400, 100mM Tris pH =8.5, 200mM CaCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.85→49.27 Å / Num. obs: 58702 / % possible obs: 99.6 % / Redundancy: 6.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.183 / Rpim(I) all: 0.078 / Rrim(I) all: 0.199 / Net I/σ(I): 7.4 / Num. measured all: 378386 / Scaling rejects: 289
Reflection shellResolution: 2.85→2.93 Å / Redundancy: 6.7 % / Rmerge(I) obs: 2.821 / Num. measured all: 30433 / Num. unique obs: 4558 / CC1/2: 0.305 / Rpim(I) all: 1.172 / Rrim(I) all: 3.059 / Net I/σ(I) obs: 0.8 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Aimless0.7.1data scaling
PHASER2.8.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MIT

6mit


Resolution: 2.85→49.265 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2917 1533 2.61 %
Rwork0.2421 57139 -
obs0.2434 58672 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 240.19 Å2 / Biso mean: 110.5674 Å2 / Biso min: 41.41 Å2
Refinement stepCycle: final / Resolution: 2.85→49.265 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10212 0 233 53 10498
Biso mean--119 81.83 -
Num. residues----1349
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 (%)
2.85-2.9420.40171420.367351815323100
2.942-3.04710.42611420.37345127526999
3.0471-3.16910.35911330.338851875320100
3.1691-3.31330.31991360.28665172530899
3.3133-3.48790.26411430.255151575300100
3.4879-3.70640.26831420.244852095351100
3.7064-3.99250.25721380.207651915329100
3.9925-4.3940.28281410.20485179532099
4.394-5.02930.26811330.19985152528599
5.0293-6.33430.30391370.259552595396100
6.3343-49.27230.28521460.23625325547199
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)
16.8522-1.1392-2.72880.6135-0.7818.7529-0.1581-0.5559-1.18980.18730.15770.29521.2906-0.07640.10580.8035-0.1286-0.09280.43860.0930.980328.4535-31.360317.6945
22.2516-3.4006-0.26625.9691-1.35273.5256-0.3251-0.2254-1.30810.3205-0.0933-1.02190.56610.21250.4250.7895-0.1144-0.0380.49210.08371.337839.026-30.40516.9888
38.48650.2059-0.85542.11680.57197.44220.03630.1361-0.1218-0.4874-0.11460.13950.3950.33830.01890.73130.01610.00650.2871-0.00730.686948.7241-13.39081.8001
46.31342.5494-1.44755.8085-0.81281.79030.38140.02740.4599-0.4347-0.42880.7336-0.39720.12230.05610.7429-0.0378-0.11550.4628-0.02740.343336.719-16.88095.9039
57.1387-2.7756-1.98314.398-0.3313.51450.28730.59780.2161-0.8255-0.1260.4726-0.3306-0.3057-0.23040.8546-0.1491-0.02360.4055-0.04460.650627.3894-19.63672.5162
65.5679-2.777-3.38582.31814.69972.13290.19040.311-1.1018-0.1607-0.40890.91290.4996-0.93160.31550.8506-0.1535-0.18830.65740.06751.140715.0338-28.248212.0589
70.53162.21570.46712.4315-1.30516.94670.0194-0.07440.8045-0.48640.0696-0.1323-0.41820.2135-0.06250.6108-0.04930.01780.49150.01770.997820.69849.389413.5858
84.54280.5084-0.91644.79722.33317.63760.6101-0.59890.60480.0033-0.44150.2218-1.15030.0538-0.06970.6861-0.06040.09410.4605-0.00530.893220.425211.58223.9973
99.1397-2.1307-0.29247.26982.21527.920.059-0.7673-0.24230.4907-0.22020.58620.2424-0.6920.15060.6675-0.04110.14060.58610.05550.777310.8302-5.275839.7981
105.3244-4.11662.51094.122-0.34723.509-0.1226-0.5181-0.5107-1.25870.83690.66480.25350.2249-0.72590.6219-0.20090.26950.764-0.11021.203112.6825-6.730931.5456
115.96310.30280.50168.87751.21955.4840.5718-0.1748-0.52780.083-0.2060.17580.31540.1967-0.10810.4441-0.0955-0.06230.4790.16740.638914.2662-2.182222.3024
127.3644-7.5991-5.22568.1056.20516.2747-0.2869-0.35080.4782-0.02590.77540.82360.0318-0.085-0.41150.5064-0.0629-0.03960.6330.04760.79456.2857-8.513320.2179
137.31570.2504-2.96913.5988-0.06168.2513-0.1261-0.16510.0598-0.16890.13530.51650.7799-0.3970.06230.5377-0.044-0.11470.5470.01110.840112.0969-3.078615.0121
142.01946.3070.12385.4391-1.59034.9061-0.56460.1621-0.632-0.30980.04190.3665-0.2034-0.53580.59450.58930.0508-0.02340.3964-0.02850.826416.72376.21916.6331
156.7923-5.29372.7297.08931.41615.62940.02330.1681-0.9645-0.65530.3241.62740.6627-0.9952-0.11970.6767-0.0526-0.00120.59290.05590.93114.8801-2.0624-0.8372
165.98690.83136.7127.7091.78028.5934-0.19110.47470.61840.8248-0.17790.21170.30141.48210.46080.6810.05550.04750.9863-0.21340.878457.27215.796246.0178
172.1592.1739-1.99679.96412.57744.5505-1.4528-0.07831.21791.1995-0.05061.52310.8766-2.28361.31270.9204-0.07840.33831.8453-0.34211.707781.559817.157571.1736
184.4316-0.55391.69783.5115-0.41521.3753-0.2043-0.79190.43720.51640.1471-0.1047-0.1803-0.07580.12111.0919-0.0855-0.32051.69380.00231.0202110.571211.168885.4095
196.0214-0.01944.25863.4292-0.13986.92270.2037-2.2119-0.09041.0837-0.1854-0.42340.3614-0.6025-0.11150.9486-0.1546-0.02091.3970.00290.706339.9465-0.834254.9976
204.9333-1.8624-0.93881.1964-0.3551.5867-0.27-1.17520.05130.0827-0.36370.2081-0.0612-0.38870.60721.155-0.1528-0.4381.93380.06991.478285.03085.979466.7398
214.7631-1.82012.13645.09121.20033.8096-0.2568-0.3166-0.08370.12180.1042-0.0549-0.61840.26790.1960.6787-0.20970.09930.7896-0.1250.731442.553114.894947.8567
225.68812.67882.47175.67132.47143.88490.1493-0.43330.3280.38180.1304-0.5816-0.1890.4456-0.23710.5769-0.06990.03180.5442-0.05880.843364.28991.203828.4554
232.1176-2.6477-2.05265.921-1.46236.2899-0.15530.29530.00130.07020.0377-0.5525-0.23390.49880.01470.741-0.23-0.23211.29610.12061.0407103.20815.3349.7341
247.58091.67875.0490.89910.6413.4035-0.3655-0.23560.5901-0.1521-0.2844-0.772-0.94851.7890.7580.9533-0.2845-0.11511.77410.14381.022894.15151.634541.4987
255.31653.75252.73544.2290.09495.3770.1899-0.5559-0.40870.402-0.2711-1.0498-0.09271.05470.14670.67190.0286-0.02440.8446-0.0860.795775.294-9.933537.3754
264.9231-4.49053.33748.01-1.96347.5591-0.1338-0.98180.34770.9364-0.3366-0.8160.558-0.20720.28390.6962-0.1362-0.03720.71830.07280.791860.2356-13.583639.3359
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 41 )A2 - 41
2X-RAY DIFFRACTION2chain 'A' and (resid 42 through 83 )A42 - 83
3X-RAY DIFFRACTION3chain 'A' and (resid 84 through 139 )A84 - 139
4X-RAY DIFFRACTION4chain 'A' and (resid 140 through 169 )A140 - 169
5X-RAY DIFFRACTION5chain 'A' and (resid 170 through 203 )A170 - 203
6X-RAY DIFFRACTION6chain 'A' and (resid 204 through 241 )A204 - 241
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 41 )B2 - 41
8X-RAY DIFFRACTION8chain 'B' and (resid 42 through 83 )B42 - 83
9X-RAY DIFFRACTION9chain 'B' and (resid 84 through 139 )B84 - 139
10X-RAY DIFFRACTION10chain 'B' and (resid 140 through 154 )B140 - 154
11X-RAY DIFFRACTION11chain 'B' and (resid 155 through 169 )B155 - 169
12X-RAY DIFFRACTION12chain 'B' and (resid 170 through 185 )B170 - 185
13X-RAY DIFFRACTION13chain 'B' and (resid 186 through 203 )B186 - 203
14X-RAY DIFFRACTION14chain 'B' and (resid 204 through 219 )B204 - 219
15X-RAY DIFFRACTION15chain 'B' and (resid 220 through 241 )B220 - 241
16X-RAY DIFFRACTION16chain 'C' and (resid 2 through 30 )C2 - 30
17X-RAY DIFFRACTION17chain 'C' and (resid 31 through 41 )C31 - 41
18X-RAY DIFFRACTION18chain 'C' and (resid 42 through 175 )C42 - 175
19X-RAY DIFFRACTION19chain 'F' and (resid 1 through 134 )F1 - 134
20X-RAY DIFFRACTION20chain 'F' and (resid 135 through 259 )F135 - 259
21X-RAY DIFFRACTION21chain 'F' and (resid 260 through 363 )F260 - 363
22X-RAY DIFFRACTION22chain 'G' and (resid 1 through 139 )G1 - 139
23X-RAY DIFFRACTION23chain 'G' and (resid 140 through 221 )G140 - 221
24X-RAY DIFFRACTION24chain 'G' and (resid 222 through 246 )G222 - 246
25X-RAY DIFFRACTION25chain 'G' and (resid 247 through 293 )G247 - 293
26X-RAY DIFFRACTION26chain 'G' and (resid 294 through 356 )G294 - 356

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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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