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- PDB-6o14: Crystal structure of the Aquifex aeolicus Wzt Carbohydrate Bindin... -

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Basic information

Entry
Database: PDB / ID: 6o14
TitleCrystal structure of the Aquifex aeolicus Wzt Carbohydrate Binding Domain
ComponentsABC transporter
KeywordsMEMBRANE PROTEIN / ABC transporter / Wzt / Wzm / O antigen / Carbohydrate Binding Domain
Function / homology
Function and homology information


ABC-type transporter activity / ATP hydrolysis activity / ATP binding / membrane
Similarity search - Function
Wzt, C-terminal / Wzt C-terminal domain / ABC transporter, teichoic acids export TagH-like / : / 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 ...Wzt, C-terminal / Wzt C-terminal domain / ABC transporter, teichoic acids export TagH-like / : / 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
Biological speciesAquifex aeolicus VF5 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsBi, Y. / Zimmer, J.
Citation
Journal: Structure / Year: 2020
Title: Structure and Ligand-Binding Properties of the O Antigen ABC Transporter Carbohydrate-Binding Domain.
Authors: Bi, Y. / Zimmer, J.
#1: Journal: Nature / Year: 2018
Title: Architecture of a channel-forming O-antigen polysaccharide ABC transporter.
Authors: Bi, Y. / Mann, E. / Whitfield, C. / Zimmer, J.
History
DepositionFeb 17, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year
Revision 1.2Oct 11, 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: ABC transporter
B: ABC transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5874
Polymers35,4032
Non-polymers1842
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-34 kcal/mol
Surface area14710 Å2
MethodPISA
2
A: ABC transporter
B: ABC transporter
hetero molecules

A: ABC transporter
B: ABC transporter
hetero molecules

A: ABC transporter
B: ABC transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,76112
Polymers106,2096
Non-polymers5536
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area17610 Å2
ΔGint-103 kcal/mol
Surface area40800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.345, 128.345, 45.158
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-603-

HOH

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Components

#1: Protein ABC transporter


Mass: 17701.443 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus VF5 (bacteria) / Strain: VF5 / Gene: abcT4, aq_1094 / Production host: Escherichia coli (E. coli) / References: UniProt: O67181
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 3.01 Å3/Da / Density % sol: 59.15 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MOPS pH 7, 1.5 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.65→28.65 Å / Num. obs: 12535 / % possible obs: 99.8 % / Redundancy: 9.2 % / CC1/2: 0.989 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.06 / Net I/av σ(I): 6.9 / Net I/σ(I): 6.9
Reflection shellResolution: 2.65→2.78 Å / Rmerge(I) obs: 1.14 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2392 / CC1/2: 0.731 / Rpim(I) all: 0.36

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2R5O

2r5o


Resolution: 2.65→28.643 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.38
RfactorNum. reflection% reflection
Rfree0.2391 614 4.9 %
Rwork0.1798 --
obs0.1828 12535 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.65→28.643 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2357 0 12 18 2387
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082423
X-RAY DIFFRACTIONf_angle_d1.1383258
X-RAY DIFFRACTIONf_dihedral_angle_d5.4711440
X-RAY DIFFRACTIONf_chiral_restr0.059347
X-RAY DIFFRACTIONf_plane_restr0.006414
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6503-2.91670.34151620.27752930X-RAY DIFFRACTION100
2.9167-3.33820.28251360.22042967X-RAY DIFFRACTION99
3.3382-4.20370.21771390.17162989X-RAY DIFFRACTION100
4.2037-28.6450.21811770.15013035X-RAY DIFFRACTION99
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)
12.46020.3058-1.70932.2776-1.67555.7777-0.22590.7594-0.6559-0.02620.40010.0670.5073-0.3003-0.12280.8151-0.0324-0.0740.74460.08440.279847.2113-38.9699-16.6055
25.6566-0.94571.70591.86163.26618.0594-0.36970.66410.499-0.29390.2896-0.23140.1270.7334-0.12030.4125-0.0364-0.05490.64240.10990.298661.6901-27.0574-7.3884
38.6691.58125.47551.67061.74167.50660.22141.0097-0.31320.0180.6361-0.52090.21210.4712-0.32940.5667-0.0357-0.04840.74490.01010.226851.5498-31.6317-16.051
43.6382-1.05870.07925.7857-0.15432.37430.68170.3402-0.5845-0.88260.19931.3298-0.1866-0.7233-0.40320.7769-0.1597-0.2691.03750.09470.512236.5177-34.8865-24.8272
53.17860.32952.58320.86431.64684.37630.2738-0.2043-0.2221-0.72630.2995-0.35320.5597-1.0984-0.97760.2137-0.0991-0.04040.68980.07260.321844.2275-32.0055-6.2519
61.90250.6472-2.68765.40663.00987.4001-0.6531-0.4211-0.53070.98030.4012-0.11541.0947-0.85050.26810.61950.00560.1010.7970.0470.217346.1981-31.56221.8725
70.7480.70540.84174.59132.28284.62520.17950.31530.303-0.8698-0.29530.4134-0.8262-1.80760.4810.70330.0026-0.06641.19150.02140.288138.62-26.5422-19.4524
81.1941-0.67662.45391.03840.20626.42030.00240.22010.0348-0.14920.18240.00130.1411-0.2018-0.06980.68810.02540.00480.6237-0.03240.205349.7429-30.2213-9.0447
96.02722.846-6.55971.6705-2.6357.8025-0.5177-0.03782.27211.52410.72461.87921.3701-1.5298-0.18130.847-0.1280.19721.392-0.06621.232229.6423-33.9947-12.6286
101.7540.16731.47731.18390.20641.11190.0318-0.0938-0.2129-0.60610.08-0.35041.5696-1.0733-0.17450.8012-0.2802-0.21051.0664-0.0134-0.288447.729-38.1534-7.2703
115.6464-2.5418-3.59872.81594.17366.22190.45590.00610.8794-0.07720.0384-0.2063-1.03860.3193-0.48760.65490.05350.02740.5340.00830.284860.2166-20.44465.2226
120.6398-0.5735-0.20668.54274.66093.27780.0832-0.09180.332-1.0068-0.0415-0.2469-1.2616-0.07220.17941.00640.0140.0980.6136-0.01480.403553.1745-2.85610.7959
132.82571.8906-1.66064.6272-0.40511.1263-0.2631-0.78470.11810.72970.0699-0.4508-1.72310.1487-0.06931.11390.08640.05170.7636-0.13390.436649.8646-3.940823.3789
146.11092.4629-0.04295.51151.13472.76740.19040.0890.455-0.19370.1180.4435-1.2368-0.3989-0.06720.92910.17510.00880.77450.03410.314542.4695-5.29339.9611
152.49191.37090.06034.65931.47294.00940.2777-0.41780.20430.1248-0.0943-0.2357-0.88880.1213-0.21780.7084-0.1002-0.00780.6079-0.05990.271656.3219-10.234616.4379
163.91473.60570.09667.90822.90575.25270.2282-0.29450.5467-0.1316-0.26610.1884-0.9587-0.2056-0.220.67150.06630.05660.703-0.01020.302548.7671-9.798813.4072
174.45480.6183-0.31644.57751.74685.4271-0.002-0.69521.47381.1939-0.4612-0.2486-0.9394-0.43-0.04991.0408-0.0525-0.06020.81310.07730.196247.2054-15.179514.1579
182.41140.8890.38434.16711.3758.7761-0.25580.4563-0.0184-0.3472-0.06970.159-0.1270.4597-0.0050.49670.0555-0.10070.64520.02030.238847.5619-24.8628-14.5421
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 253 through 265 )
2X-RAY DIFFRACTION2chain 'A' and (resid 266 through 278 )
3X-RAY DIFFRACTION3chain 'A' and (resid 279 through 288 )
4X-RAY DIFFRACTION4chain 'A' and (resid 289 through 295 )
5X-RAY DIFFRACTION5chain 'A' and (resid 296 through 302 )
6X-RAY DIFFRACTION6chain 'A' and (resid 303 through 313 )
7X-RAY DIFFRACTION7chain 'A' and (resid 314 through 325 )
8X-RAY DIFFRACTION8chain 'A' and (resid 326 through 350 )
9X-RAY DIFFRACTION9chain 'A' and (resid 351 through 358 )
10X-RAY DIFFRACTION10chain 'A' and (resid 359 through 371 )
11X-RAY DIFFRACTION11chain 'A' and (resid 372 through 381 )
12X-RAY DIFFRACTION12chain 'A' and (resid 382 through 397 )
13X-RAY DIFFRACTION13chain 'B' and (resid 253 through 265 )
14X-RAY DIFFRACTION14chain 'B' and (resid 266 through 288 )
15X-RAY DIFFRACTION15chain 'B' and (resid 289 through 325 )
16X-RAY DIFFRACTION16chain 'B' and (resid 326 through 351 )
17X-RAY DIFFRACTION17chain 'B' and (resid 352 through 381 )
18X-RAY DIFFRACTION18chain 'B' and (resid 382 through 395 )

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