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- PDB-6oih: Crystal structure of O-antigen polysaccharide ABC-transporter -

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Basic information

Entry
Database: PDB / ID: 6oih
TitleCrystal structure of O-antigen polysaccharide ABC-transporter
Components
  • ABC transporterATP-binding cassette transporter
  • Transport permease protein
KeywordsTRANSPORT PROTEIN / O-antigen polysaccharide ABC transporter
Function / homology
Function and homology information


lipopolysaccharide transport / ABC-type transporter activity / ATP hydrolysis activity / ATP binding / membrane / plasma membrane
Similarity search - Function
Wzt, C-terminal / Wzt C-terminal domain / : / ABC transporter integral membrane type-2 domain profile. / ABC transporter, teichoic acids export TagH-like / ABC-2 type transporter / ABC-2 type transporter / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter ...Wzt, C-terminal / Wzt C-terminal domain / : / ABC transporter integral membrane type-2 domain profile. / ABC transporter, teichoic acids export TagH-like / ABC-2 type transporter / ABC-2 type transporter / 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. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ABC transporter / Transport permease protein
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.85 Å
AuthorsBi, Y. / Zimmer, J.
CitationJournal: Nature / Year: 2018
Title: Architecture of a channel-forming O-antigen polysaccharide ABC transporter.
Authors: Bi, Y. / Mann, E. / Whitfield, C. / Zimmer, J.
History
DepositionApr 9, 2019Deposition site: RCSB / Processing site: RCSB
SupersessionApr 17, 2019ID: 6AN7
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: ABC transporter
B: ABC transporter
D: Transport permease protein
C: Transport permease protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,80712
Polymers114,9714
Non-polymers1,8358
Water0
1
A: ABC transporter
D: Transport permease protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1745
Polymers57,4862
Non-polymers6883
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ABC transporter
C: Transport permease protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6337
Polymers57,4862
Non-polymers1,1475
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)228.116, 228.116, 228.116
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132

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Components

#1: Protein ABC transporter / ATP-binding cassette transporter


Mass: 27660.098 Da / Num. of mol.: 2 / Fragment: nucleotide-binding domain (UNP residues 3-236)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria)
Strain: VF5 / Gene: abcT4, aq_1094 / Production host: Escherichia coli (E. coli) / References: UniProt: O67181
#2: Protein Transport permease protein


Mass: 29825.596 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria)
Strain: VF5 / Gene: abcT3, aq_1095 / Production host: Escherichia coli (E. coli) / References: UniProt: O67182
#3: Chemical
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE / Lauryldimethylamine oxide


Mass: 229.402 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM

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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: 4.35 Å3/Da / Density % sol: 71.73 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 32% PEG400, 0.05 M sodium acetate, 0.1 M magnesium acetate, 3.6 mM decyl beta-D-maltoside

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 24, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.85→25 Å / Num. obs: 19830 / % possible obs: 99.6 % / Redundancy: 9.6 % / Rpim(I) all: 0.076 / Net I/σ(I): 7.6
Reflection shellResolution: 3.85→4.22 Å / Num. unique obs: 4618 / Rpim(I) all: 0.727

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.85→24.889 Å / SU ML: 0.56 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.34
RfactorNum. reflection% reflection
Rfree0.2966 1007 5.11 %
Rwork0.2188 --
obs0.2226 19719 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.85→24.889 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7968 0 52 0 8020
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038233
X-RAY DIFFRACTIONf_angle_d0.70211136
X-RAY DIFFRACTIONf_dihedral_angle_d2.8534792
X-RAY DIFFRACTIONf_chiral_restr0.0441261
X-RAY DIFFRACTIONf_plane_restr0.0031338
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8504-4.05250.37481520.33482625X-RAY DIFFRACTION100
4.0525-4.30520.35731610.3072586X-RAY DIFFRACTION100
4.3052-4.63570.28441480.26362604X-RAY DIFFRACTION100
4.6357-5.09860.28691340.23562654X-RAY DIFFRACTION100
5.0986-5.82810.3581390.26192664X-RAY DIFFRACTION100
5.8281-7.31170.36851480.26632704X-RAY DIFFRACTION100
7.3117-24.890.2221250.14732875X-RAY DIFFRACTION100
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)
14.5627-3.1588-4.69658.95050.7175.68711.1430.29961.3393-0.56660.28260.7889-0.3547-0.9549-1.3021.4154-0.1029-0.14981.92610.14991.9807-6.338725.279766.1582
29.3271-3.323.0655.22843.19347.1711-0.7353-0.8723-0.9658-0.96571.04490.0924-0.547-0.6103-0.61641.1397-0.32970.34811.2113-0.05751.93298.254912.829159.9536
37.96694.63730.2933.5240.16484.1212-0.8068-0.6209-2.5767-0.21770.3445-1.09930.32-0.2875-0.03041.56030.1510.42071.7395-0.02681.96-1.93310.873856.4772
46.8202-0.4915-3.66326.1442-3.39524.1453-0.1481-0.647-0.68650.23680.7035-0.60730.0983-0.4395-0.72871.7784-0.0856-0.22081.7013-0.60471.5854-3.6543-12.331453.3986
52.93721.219-0.21212.9884-0.98860.4192-0.3156-2.28940.53210.29110.0366-2.56960.44730.0893-0.19382.0242-0.29350.41452.3279-0.60142.144710.8655-7.112857.5357
68.3931-2.9353-6.16946.7218-2.06998.1581-0.9013-2.1074-2.36360.2953-0.3182-1.5951.97211.63340.14661.11430.2353-0.3841.8178-0.3872.550318.24397.79867.3897
77.89613.11652.60575.38363.39863.2507-1.08460.71680.0520.77990.3082-1.36911.57460.98580.09362.13270.3229-0.28470.86960.2151.3031-15.8042-26.706375.4563
89.11980.53682.82518.31870.52175.5559-0.3175-0.2068-0.8171.82920.5590.11040.6665-0.0581-0.31341.7270.3318-0.13611.2487-0.03321.163-14.6681-24.788977.7002
93.24371.62940.2536.4440.47595.48880.2376-0.1959-0.72871.9515-0.7976-2.1678-1.2666-0.26550.0481.5509-0.2766-0.7921.5517-0.14211.1228-12.33581.192681.8274
109.18983.0475-4.983.336-3.64454.4086-0.7863-1.50560.07252.96980.4662-2.1174-0.96322.39610.16971.5226-0.327-0.65842.3818-0.43432.2796-10.44535.913593.6008
118.60398.1135-5.62549.2683-4.23364.3832-1.42471.4416-1.23440.0602-0.7809-2.8504-1.31033.73251.51291.4428-0.127-0.70242.383-0.33082.215-3.49996.930681.6554
128.862-2.41191.31694.60293.31924.941.05833.0627-1.04990.135-2.5706-0.8006-1.5364-1.7421.36961.64220.3498-0.60252.2922-0.03591.6886-1.889-9.431487.0918
138.8113-4.6539-1.23228.2265-1.84581.25052.23662.6451-1.81540.25-2.7469-1.6790.4735-0.51710.01013.3101-0.1974-1.30941.97430.47732.10533.4979-4.940794.1386
142.3701-0.26142.24978.68881.11224.42551.1948-0.7041-0.31781.2341-0.2552-3.0021-0.04331.1082-0.14872.38340.5561-1.05271.9046-0.53882.92794.6512-16.99988.8674
156.60696.32417.46386.06867.09098.5823-1.02671.0378-2.28741.22893.4652-1.0259-1.08893.9159-2.59231.88980.5951-0.51432.3924-0.16171.70090.3927-29.030285.72
166.1382-3.3941-6.58374.69222.42127.5937-3.4577-0.97171.414-0.1473-3.15351.7394-3.4578-1.6894.34392.49840.6868-1.47072.977-0.99663.996110.0948-30.352281.2217
175.71033.4663-3.58695.68361.38745.80861.729-0.6637-1.05711.2618-1.88710.30651.49390.0263-0.09151.1437-0.4416-0.42472.4990.5261.2037-17.8915-3.712649.8411
187.2324-0.60321.44027.3870.71676.2483-0.36910.5019-0.99580.7627-0.24021.2694-1.1733-0.61320.23291.2937-0.2831-0.39581.5719-0.08810.9196-42.1643-7.40550.8392
196.56533.45373.80935.45563.36977.6274-0.40040.54340.516-0.87990.55680.1466-1.14820.0626-0.02591.3204-0.1373-0.27641.15290.37171.1327-29.38634.669348.6632
205.12391.26843.0328.79474.07996.64950.4181.49620.429-0.08110.18390.42310.68320.8354-0.59251.28950.1785-0.07490.97690.21770.7087-30.244712.283242.3887
216.41062.5508-4.3164.67452.45557.7435-0.7771.03410.8787-0.6567-0.1782-0.5155-0.1638-1.7642-0.73371.60460.0593-0.2330.32690.43181.5968-39.705316.088954.898
223.0493-0.8271.34741.4812-0.3183.12-0.11270.61842.2020.89710.23430.2371-0.89892.03430.15461.8849-0.0817-0.9571.94440.68022.6185-44.371125.048646.2689
235.32331.5993-4.1993.48572.45137.9269-1.97582.38642.60250.14290.11760.2227-1.8445-0.78550.16821.7715-0.3443-0.4131.69720.9591.5652-42.663112.37538.6633
244.57930.54324.81724.04110.36164.94970.16180.92430.9197-0.1774-0.1478-1.099-0.5644-0.2963-0.19521.53990.0380.01181.34590.05571.3613-20.494521.160846.0389
254.9975-2.51733.30853.5185-4.19099.1112-0.6496-0.68781.2861-0.4350.9598-0.3894-0.8060.31960.77241.0590.35680.17450.86870.5011.3028-26.53119.96377.9034
267.83463.255-3.6925.2105-1.91986.35230.64361.83120.6289-2.32340.00092.7714-0.2446-1.3683-1.13381.98730.595-0.05320.90.28452.1613-48.903417.975463.3048
274.0186-1.9262-0.93063.59210.7384.3631-0.0588-0.20481.25730.1940.2306-0.37330.326-0.646-0.41221.03560.0350.14261.04330.12371.0855-35.1815-1.233172.0246
288.2156-3.33623.39857.5095-3.06982.8875-0.0752-0.44550.72970.53230.05620.4243-0.4428-0.48370.21071.48720.22670.17951.2335-0.04720.9038-43.24148.236178.5335
293.9032-0.4131-2.45333.04122.05448.16710.22170.2271-0.0426-0.71050.4130.9065-0.8092-0.7598-0.64220.8812-0.1301-0.13790.73790.08151.0235-46.4697-7.262473.0076
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 36 )
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 76 )
3X-RAY DIFFRACTION3chain 'A' and (resid 77 through 99 )
4X-RAY DIFFRACTION4chain 'A' and (resid 100 through 157 )
5X-RAY DIFFRACTION5chain 'A' and (resid 158 through 189 )
6X-RAY DIFFRACTION6chain 'A' and (resid 190 through 238 )
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 16 )
8X-RAY DIFFRACTION8chain 'B' and (resid 17 through 84 )
9X-RAY DIFFRACTION9chain 'B' and (resid 85 through 114 )
10X-RAY DIFFRACTION10chain 'B' and (resid 115 through 129 )
11X-RAY DIFFRACTION11chain 'B' and (resid 130 through 157 )
12X-RAY DIFFRACTION12chain 'B' and (resid 158 through 173 )
13X-RAY DIFFRACTION13chain 'B' and (resid 174 through 189 )
14X-RAY DIFFRACTION14chain 'B' and (resid 190 through 207 )
15X-RAY DIFFRACTION15chain 'B' and (resid 208 through 224 )
16X-RAY DIFFRACTION16chain 'B' and (resid 225 through 239 )
17X-RAY DIFFRACTION17chain 'D' and (resid 2 through 19 )
18X-RAY DIFFRACTION18chain 'D' and (resid 20 through 56 )
19X-RAY DIFFRACTION19chain 'D' and (resid 57 through 129 )
20X-RAY DIFFRACTION20chain 'D' and (resid 130 through 165 )
21X-RAY DIFFRACTION21chain 'D' and (resid 166 through 193 )
22X-RAY DIFFRACTION22chain 'D' and (resid 194 through 203 )
23X-RAY DIFFRACTION23chain 'D' and (resid 204 through 223 )
24X-RAY DIFFRACTION24chain 'D' and (resid 224 through 255 )
25X-RAY DIFFRACTION25chain 'C' and (resid 2 through 29 )
26X-RAY DIFFRACTION26chain 'C' and (resid 30 through 57 )
27X-RAY DIFFRACTION27chain 'C' and (resid 58 through 99 )
28X-RAY DIFFRACTION28chain 'C' and (resid 100 through 133 )
29X-RAY DIFFRACTION29chain 'C' and (resid 134 through 255 )

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