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- PDB-6an5: Crystal Structure of The Nucelotide Binding Domain of an O-antige... -

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Basic information

Entry
Database: PDB / ID: 6an5
TitleCrystal Structure of The Nucelotide Binding Domain of an O-antigen polysaccharide ABC-transporter
ComponentsABC transporter
KeywordsTRANSPORT PROTEIN / Nucleotide Binding Domain of abcT4
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.512 Å
AuthorsZimmer, J. / Bi, Y.
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
DepositionAug 12, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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
B: ABC transporter


Theoretical massNumber of molelcules
Total (without water)55,3202
Polymers55,3202
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-12 kcal/mol
Surface area22030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.210, 97.210, 103.690
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 45 or resid 47...
21(chain B and (resid 2 through 11 or resid 34...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEGLUGLU(chain A and (resid 2 through 45 or resid 47...AA2 - 451 - 44
12GLYGLYASPASP(chain A and (resid 2 through 45 or resid 47...AA47 - 13246 - 131
13PHEPHEGLYGLY(chain A and (resid 2 through 45 or resid 47...AA134 - 172133 - 171
14ALAALAALAALA(chain A and (resid 2 through 45 or resid 47...AA174173
15PHEPHELYSLYS(chain A and (resid 2 through 45 or resid 47...AA176 - 236175 - 235
21ILEILETYRTYR(chain B and (resid 2 through 11 or resid 34...BB2 - 111 - 10
22LEULEUGLUGLU(chain B and (resid 2 through 11 or resid 34...BB34 - 4533 - 44
23GLYGLYASPASP(chain B and (resid 2 through 11 or resid 34...BB47 - 13246 - 131
24PHEPHEGLYGLY(chain B and (resid 2 through 11 or resid 34...BB134 - 172133 - 171
25ALAALAALAALA(chain B and (resid 2 through 11 or resid 34...BB174173
26PHEPHELYSLYS(chain B and (resid 2 through 11 or resid 34...BB176 - 236175 - 235

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Components

#1: Protein ABC transporter


Mass: 27660.098 Da / Num. of mol.: 2 / Fragment: Nucelotide Binding Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria)
Strain: VF5 / Gene: abcT4, aq_1094 / Plasmid: pETDuet / Production host: Escherichia coli (E. coli) / Strain (production host): C43 / References: UniProt: O67181

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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: 2.61 Å3/Da / Density % sol: 52.85 % / Mosaicity: 0.81 °
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: The crystal was grew in the presence of 0.4M Magnesium Nitrate, 17.5% PEG 8000, 0.1M Tris pH8.5 by sitting-drop vapor diffusion at 17C. The cryo-protection condition is 25% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 24, 2016 / Details: 4*4 mosiac
RadiationMonochromator: double crystal - liquid nitrogen cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.51→39.25 Å / Num. obs: 13640 / % possible obs: 99.8 % / Redundancy: 5.4 % / CC1/2: 0.993 / Rmerge(I) obs: 0.175 / Rpim(I) all: 0.083 / Rrim(I) all: 0.195 / Net I/σ(I): 6.6
Reflection shell

Diffraction-ID: 1 / Resolution: 3.51→3.85 Å

Redundancy (%)Num. unique obsCC1/2Rpim(I) allRrim(I) all% possible allRmerge(I) obs
5.517410.6280.4020.942100
4.85380.9970.0260.06396.50.057

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
Aimlessdata reduction
PHENIXphasing
RefinementResolution: 3.512→27.119 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 0.04 / Phase error: 34.62
RfactorNum. reflection% reflection
Rfree0.3054 395 5.29 %
Rwork0.2449 --
obs0.2484 13640 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 210.55 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3.512→27.119 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3585 0 0 0 3585
Num. residues----451
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053645
X-RAY DIFFRACTIONf_angle_d0.8134898
X-RAY DIFFRACTIONf_chiral_restr0.052551
X-RAY DIFFRACTIONf_plane_restr0.005614
X-RAY DIFFRACTIONf_dihedral_angle_d2.2132194
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1952X-RAY DIFFRACTION6.66TORSIONAL
12B1952X-RAY DIFFRACTION6.66TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.5121-3.78260.39781500.326925532703
3.7826-4.1620.36951440.286226082752
4.162-4.76150.28841290.227625862715
4.7615-5.98830.32071560.246725772733
5.9883-27.11990.2571430.214925942737
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)
15.13522.252-1.63451.8856-0.38684.2867-0.16-0.6175-1.30310.44160.04850.64620.44570.07780.11910.96370.14680.470.91230.31851.0996-40.187723.3918-3.3631
26.65442.0485-0.36795.81280.19835.84920.124-0.4821-0.1359-0.3941-0.07770.70270.37120.45990.2320.37710.0745-0.03250.57720.00190.6649-20.532138.49-17.5876
33.34321.1625-1.4685.65480.29940.71160.0231-1.4224-0.12561.48990.20460.4532-0.26030.4547-0.16080.8947-0.03580.14511.5211-0.00070.8016-33.2135.83243.5634
43.13590.9583.11592.8587-0.04094.0479-0.36931.05690.12270.07050.2716-0.47890.42341.383-0.00090.44410.18920.18410.98820.05630.7922-2.598536.1171-27.4296
53.51412.35250.03677.03010.75340.7486-0.344-0.5429-1.72820.29740.36940.0104-0.01140.5231-0.05420.80180.4596-0.10581.14890.29221.0154-1.726125.9338-8.7022
67.519-1.08136.30741.5752-0.31685.4045-0.4792-1.4644-0.4685-0.1143-0.7185-1.00540.0052-0.3583-1.8011.68440.46520.60160.70631.1831.8462-15.555812.271.2669
75.67163.5102-0.57112.3140.20022.61180.3853-1.6344-0.47850.1604-0.63070.08480.37380.66330.22271.03540.29710.00861.4080.34371.0471-4.848128.33935.6952
87.21270.8188-0.91476.34011.46323.6332-0.8288-0.66480.54280.74220.87080.2004-0.41210.562-0.11180.92710.311-0.22191.6142-0.24490.96214.601444.6468-2.9363
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 84 )A2 - 84
2X-RAY DIFFRACTION2chain 'A' and (resid 85 through 157 )A85 - 157
3X-RAY DIFFRACTION3chain 'A' and (resid 158 through 236 )A158 - 236
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 40 )B2 - 40
5X-RAY DIFFRACTION5chain 'B' and (resid 41 through 99 )B41 - 99
6X-RAY DIFFRACTION6chain 'B' and (resid 100 through 158 )B100 - 158
7X-RAY DIFFRACTION7chain 'B' and (resid 159 through 207 )B159 - 207
8X-RAY DIFFRACTION8chain 'B' and (resid 208 through 239 )B208 - 239

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