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- PDB-5wht: Crystal structure of 3'SL bound PltB -

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Basic information

Entry
Database: PDB / ID: 5wht
TitleCrystal structure of 3'SL bound PltB
ComponentsPutative pertussis-like toxin subunit
KeywordsTOXIN / bacterial toxin / glycan
Function / homology
Function and homology information


extracellular region
Similarity search - Function
Bordetella pertussis toxin B, subunit 2/3, C-terminal / Pertussis toxin, subunit 2 and 3, C-terminal domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / Enterotoxin / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
3'-sialyl-alpha-lactose / ACETATE ION / DI(HYDROXYETHYL)ETHER / N-acetyl-alpha-neuraminic acid / Pertussis-like toxin subunit
Similarity search - Component
Biological speciesSalmonella typhi (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.932 Å
AuthorsGao, X. / Galan, J.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI079022 United States
CitationJournal: Nat Microbiol / Year: 2017
Title: Evolution of host adaptation in the Salmonella typhoid toxin.
Authors: Gao, X. / Deng, L. / Stack, G. / Yu, H. / Chen, X. / Naito-Matsui, Y. / Varki, A. / Galan, J.E.
History
DepositionJul 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative pertussis-like toxin subunit
B: Putative pertussis-like toxin subunit
C: Putative pertussis-like toxin subunit
D: Putative pertussis-like toxin subunit
E: Putative pertussis-like toxin subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,46322
Polymers76,7375
Non-polymers2,72617
Water8,611478
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15070 Å2
ΔGint-32 kcal/mol
Surface area22310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.379, 95.682, 117.173
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 5 molecules ABCDE

#1: Protein
Putative pertussis-like toxin subunit


Mass: 15347.406 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhi (bacteria) / Gene: STY1891, t1107 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8Z6A3

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Sugars , 3 types, 4 molecules

#2: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose / 3'-sialyl-alpha-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 633.552 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 3'-sialyl-alpha-lactose
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1a_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a4-b1_b3-c2WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#3: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 471.411 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2/a3-b2WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}LINUCSPDB-CARE
#5: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H19NO9
IdentifierTypeProgram
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 491 molecules

#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 478 / 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: 2.21 Å3/Da / Density % sol: 44.23 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Feb 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. obs: 51433 / % possible obs: 99.61 % / Redundancy: 5.3 % / Net I/σ(I): 14.41

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
HKL-2000data collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RHR

4rhr


Resolution: 1.932→23.437 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.82
RfactorNum. reflection% reflection
Rfree0.2112 2466 4.85 %
Rwork0.1602 --
obs0.1627 50838 98.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.932→23.437 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4440 0 184 478 5102
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064764
X-RAY DIFFRACTIONf_angle_d1.086474
X-RAY DIFFRACTIONf_dihedral_angle_d14.7741616
X-RAY DIFFRACTIONf_chiral_restr0.071732
X-RAY DIFFRACTIONf_plane_restr0.004810
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9318-1.96890.27671220.20142659X-RAY DIFFRACTION98
1.9689-2.00910.26031590.19342651X-RAY DIFFRACTION99
2.0091-2.05280.21721280.16872682X-RAY DIFFRACTION100
2.0528-2.10050.28021310.18092685X-RAY DIFFRACTION99
2.1005-2.1530.23431310.17362685X-RAY DIFFRACTION99
2.153-2.21120.24421490.16732648X-RAY DIFFRACTION99
2.2112-2.27620.22231160.17242710X-RAY DIFFRACTION99
2.2762-2.34960.25531420.17372658X-RAY DIFFRACTION98
2.3496-2.43350.22911350.19482643X-RAY DIFFRACTION98
2.4335-2.53080.28611360.18352657X-RAY DIFFRACTION98
2.5308-2.64580.19081280.18072628X-RAY DIFFRACTION97
2.6458-2.78510.30271390.18532619X-RAY DIFFRACTION97
2.7851-2.95930.21811370.18972629X-RAY DIFFRACTION96
2.9593-3.18730.21561270.17532718X-RAY DIFFRACTION98
3.1873-3.50710.22361530.15082728X-RAY DIFFRACTION100
3.5071-4.01230.15451410.13822761X-RAY DIFFRACTION99
4.0123-5.04680.16561320.11632749X-RAY DIFFRACTION99
5.0468-23.43880.18531600.15452862X-RAY DIFFRACTION98
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)
18.4863-5.5885-4.49414.76283.64713.0326-0.4351-0.28950.07540.23340.3932-0.12640.19350.18080.02250.2720.0217-0.01070.2420.03530.2031-3.529717.63287.2199
25.72173.1127-4.62673.6457-3.84786.74110.0669-0.16870.09130.1749-0.08120.0422-0.24210.21020.00420.1885-0.0042-0.01910.1733-0.0130.1201-10.157431.2463-0.1875
36.9153-5.6479-4.93675.22314.37883.73010.08720.45330.5212-0.1855-0.0699-0.41070.0846-0.0565-0.16540.1529-0.0198-0.01660.2090.02140.1621-0.551129.2856-2.8043
42.2201-0.71830.68660.4571-0.65231.3895-0.02390.6208-0.1017-0.07730.0240.06760.0949-0.0584-0.01990.206-0.00950.00620.21630.0050.18-8.46622.9581-6.877
53.87962.7393-0.21655.9432-0.99631.9010.0255-0.118-0.0350.4085-0.05-0.3418-0.2390.21270.02970.2310.0116-0.01070.2521-0.00880.1266-4.368628.55762.9458
65.04822.8964-3.18257.0309-0.13667.41170.5969-1.1534-0.44941.3133-0.15220.4772-0.4437-0.972-0.39170.3891-0.03420.03890.39650.09060.3304-14.452612.16695.958
72.00011.999822.00021.99991.99993.87724.7313-0.8589-4.86250.36118.8558-2.6317-6.228-4.26340.66050.5591-0.01310.49970.42930.9734-4.188213.142212.2595
83.6008-5.0521.72727.8999-0.89895.2889-0.0042-0.19320.58840.4813-0.0525-0.3686-0.87110.25180.08270.341-0.0750.01080.2298-0.00070.1974-5.97946.3434-7.1469
97.2288-1.1685-6.03870.11080.91825.01420.06730.309-0.03610.0061-0.08990.077-0.1873-0.4321-0.05050.24310.0240.02150.21220.0440.2398-12.919540.5682-22.8151
104.83990.711-1.48161.7536-0.19932.75320.06380.09830.05020.0796-00.0156-0.0226-0.1417-0.0520.22170.009-0.00260.17090.04620.1203-11.181239.0356-15.4848
112.04961.3964-0.96794.5223-4.3378.13860.03820.09620.28830.1338-0.1314-0.0595-0.58140.34870.0810.20570.00180.03420.15280.0330.2227-7.167446.8494-21.5259
124.2444.2082-3.83494.548-4.75966.36740.8703-0.78421.04870.8193-0.3530.1275-0.80140.1017-0.48050.3242-0.06150.05020.2881-0.05820.32-14.514541.8461-0.1777
138.5479-2.2664-7.02353.21871.17837.5155-0.26680.1112-0.62930.17670.02870.19070.5949-0.03310.270.2631-0.0075-0.00930.1687-0.0450.2377-9.9642-4.7427-14.9054
148.71166.70092.87845.95452.92371.56490.1117-0.1607-0.1580.0048-0.1722-0.12940.0507-0.06060.06260.19230.0130.00840.17170.03950.1498-9.77399.9148-4.4916
155.59980.1537-0.4782.84760.57222.9127-0.03390.0272-0.0175-0.02830.0428-0.08970.1099-0.0698-0.01030.1732-0.0079-0.00720.1308-0.02640.0937-11.69866.6488-10.9461
164.40021.05673.37172.02651.3375.60170.0008-0.2446-0.16110.2488-0.0144-0.09340.13640.04110.03080.22650.01410.01420.19250.02720.216-5.04692.8175-3.3541
178.7961-0.6011-2.26796.008-0.5276.10570.33470.5304-1.18820.2419-0.65380.99851.1968-1.56040.35770.4686-0.1575-0.02020.55-0.18630.5044-21.4741-2.8068-19.1913
188.2454-0.7906-3.00775.63221.22315.59020.03741.0081-0.3888-0.48330.00450.20380.9391-0.0674-0.02380.4776-0.0132-0.03550.3857-0.05710.2567-10.845911.3788-44.7087
193.7977-1.10010.7781.8722-1.45952.0614-0.0404-0.1521-0.0223-0.19750.17260.16650.1787-0.2354-0.15790.2617-0.0258-0.00060.2231-0.06760.2139-16.24965.5807-28.231
207.5107-0.9921-2.31952.6431-1.2592.1739-0.31890.3938-0.2895-0.29410.29040.34690.2201-0.10330.04340.2502-0.0272-0.03690.1605-0.03580.211-16.28054.3528-31.3519
214.417-0.132-1.8821.0583-0.70462.726-0.15790.2350.0869-0.06450.08340.0125-0.0609-0.10840.07630.25940.002-0.02610.1931-0.03870.1716-13.415814.7374-28.0136
222.298-1.69620.01023.1445-0.41191.2494-0.04940.1542-0.1282-0.280.09120.10070.164-0.0158-0.02810.2803-0.0431-0.01470.2556-0.05810.2361-13.63213.9362-33.2205
238.64942.4857-4.23647.36311.60375.73950.50550.6398-0.5079-0.72290.04290.4159-0.1785-0.9518-0.44580.3881-0.0138-0.12220.50690.04490.4112-25.623817.264-41.1261
245.47712.8033-1.31111.4289-0.57483.35670.01910.35340.6508-0.35240.10870.2319-0.2957-0.0595-0.07050.35930.0055-0.02170.22020.06890.2771-13.707341.6552-37.9376
256.7711-4.9332-0.85363.87130.55520.54370.22050.46140.1327-0.4839-0.2037-0.0908-0.0196-0.0684-0.04720.28170.0036-0.00130.28130.02420.2224-16.753323.9541-36.8541
266.9595-0.8283-2.55014.30321.20052.58210.11610.425-0.2692-0.4652-0.0920.2648-0.0979-0.2359-0.02440.3111-0.0075-0.02760.22380.04580.1462-15.520230.4125-39.314
274.13292.5618-3.21752.6356-1.4443.0797-0.3185-0.7365-0.45970.25660.0331-0.26280.02070.20260.24250.26830.02380.00750.1980.04330.2122-14.748127.8854-27.8614
283.9321-0.0469-0.81893.3831-1.30121.9121-0.04890.616-0.0309-0.4601-0.0121-0.02420.0159-0.14540.06540.2743-0.0302-0.0540.2558-0.01250.1634-15.080732.8614-39.8013
298.4574-1.1033-4.53124.671-3.9757.0203-0.19430.777-0.7284-1.3080.32270.16140.0936-0.2694-0.11670.5386-0.0019-0.01490.395-0.04940.2265-14.767223.694-47.0945
305.6189-0.6024-3.72757.46243.37798.3008-0.09040.0120.1081-0.3682-0.18571.101-0.3613-0.27020.22790.24520.0019-0.0660.220.02350.2976-19.621540.9713-30.7788
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 24 through 36 )
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 66 )
3X-RAY DIFFRACTION3chain 'A' and (resid 67 through 76 )
4X-RAY DIFFRACTION4chain 'A' and (resid 77 through 95 )
5X-RAY DIFFRACTION5chain 'A' and (resid 96 through 127 )
6X-RAY DIFFRACTION6chain 'A' and (resid 128 through 137 )
7X-RAY DIFFRACTION7chain 'A' and (resid 138 through 138 )
8X-RAY DIFFRACTION8chain 'B' and (resid 24 through 36 )
9X-RAY DIFFRACTION9chain 'B' and (resid 37 through 59 )
10X-RAY DIFFRACTION10chain 'B' and (resid 60 through 104 )
11X-RAY DIFFRACTION11chain 'B' and (resid 105 through 127 )
12X-RAY DIFFRACTION12chain 'B' and (resid 128 through 138 )
13X-RAY DIFFRACTION13chain 'C' and (resid 24 through 36 )
14X-RAY DIFFRACTION14chain 'C' and (resid 37 through 59 )
15X-RAY DIFFRACTION15chain 'C' and (resid 60 through 104 )
16X-RAY DIFFRACTION16chain 'C' and (resid 105 through 127 )
17X-RAY DIFFRACTION17chain 'C' and (resid 128 through 137 )
18X-RAY DIFFRACTION18chain 'D' and (resid 24 through 31 )
19X-RAY DIFFRACTION19chain 'D' and (resid 32 through 59 )
20X-RAY DIFFRACTION20chain 'D' and (resid 60 through 76 )
21X-RAY DIFFRACTION21chain 'D' and (resid 77 through 95 )
22X-RAY DIFFRACTION22chain 'D' and (resid 96 through 127 )
23X-RAY DIFFRACTION23chain 'D' and (resid 128 through 137 )
24X-RAY DIFFRACTION24chain 'E' and (resid 24 through 36 )
25X-RAY DIFFRACTION25chain 'E' and (resid 37 through 59 )
26X-RAY DIFFRACTION26chain 'E' and (resid 60 through 78 )
27X-RAY DIFFRACTION27chain 'E' and (resid 79 through 95 )
28X-RAY DIFFRACTION28chain 'E' and (resid 96 through 110 )
29X-RAY DIFFRACTION29chain 'E' and (resid 111 through 120 )
30X-RAY DIFFRACTION30chain 'E' and (resid 121 through 137 )

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  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

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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