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- PDB-4rhs: Crystal structure of GD2 bound PltB -

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Basic information

Entry
Database: PDB / ID: 4rhs
TitleCrystal structure of GD2 bound PltB
ComponentsPutative pertussis-like toxin subunit
KeywordsSUGAR BINDING PROTEIN / sugar binding motif / sugar binding / sugar
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
ACETATE ION / Pertussis-like toxin subunit
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhi (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9211 Å
AuthorsGao, X. / Wang, J. / Galan, J.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2014
Title: Host adaptation of a bacterial toxin from the human pathogen salmonella typhi.
Authors: Deng, L. / Song, J. / Gao, X. / Wang, J. / Yu, H. / Chen, X. / Varki, N. / Naito-Matsui, Y. / Galan, J.E. / Varki, A.
History
DepositionOct 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / 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 / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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)69,8149
Polymers68,1715
Non-polymers1,6434
Water7,566420
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12360 Å2
ΔGint-35 kcal/mol
Surface area22290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.257, 96.751, 104.002
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Putative pertussis-like toxin subunit


Mass: 13634.195 Da / Num. of mol.: 5 / Fragment: UNP Residue 24-137
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhi (bacteria)
Gene: STY1891, t1107 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8Z6A3
#2: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 762.666 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-8DNeup5Aca2-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-2/a3-b2_b8-c2WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{[(8+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 420 / 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: 2.52 Å3/Da / Density % sol: 51.17 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 26% (w/v) PEG1500 and 0.1 M sodium acetate, pH5.0 soaked with GD2, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: May 23, 2014
RadiationMonochromator: si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.92→26.05 Å / Num. obs: 51223 / % possible obs: 95.61 % / Observed criterion σ(F): 1.35
Reflection shellResolution: 1.92→1.99 Å / % possible all: 93.04

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASESphasing
PHENIX(phenix.refine: dev_1701)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9211→26.046 Å / SU ML: 0.22 / σ(F): 1.35 / Phase error: 22.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2054 2571 5.06 %RANDOM
Rwork0.1747 ---
obs0.1763 50854 95.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9211→26.046 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4430 0 112 420 4962
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074674
X-RAY DIFFRACTIONf_angle_d1.1626367
X-RAY DIFFRACTIONf_dihedral_angle_d12.3861583
X-RAY DIFFRACTIONf_chiral_restr0.043721
X-RAY DIFFRACTIONf_plane_restr0.006796
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9211-1.9580.35241500.28162505X-RAY DIFFRACTION92
1.958-1.9980.29061450.24552631X-RAY DIFFRACTION94
1.998-2.04140.22621250.20782610X-RAY DIFFRACTION94
2.0414-2.08890.23721350.20052624X-RAY DIFFRACTION95
2.0889-2.14110.22931430.18642611X-RAY DIFFRACTION94
2.1411-2.19890.2131370.19672640X-RAY DIFFRACTION95
2.1989-2.26360.3191360.24722672X-RAY DIFFRACTION96
2.2636-2.33660.28911500.21122581X-RAY DIFFRACTION94
2.3366-2.42010.20961370.1882709X-RAY DIFFRACTION96
2.4201-2.51690.21521510.19092642X-RAY DIFFRACTION96
2.5169-2.63140.2621260.18832707X-RAY DIFFRACTION96
2.6314-2.76990.23931410.19952667X-RAY DIFFRACTION96
2.7699-2.94330.22341580.21372579X-RAY DIFFRACTION93
2.9433-3.17020.2421330.18192713X-RAY DIFFRACTION97
3.1702-3.48850.20131360.15752802X-RAY DIFFRACTION98
3.4885-3.99170.15851530.14872793X-RAY DIFFRACTION98
3.9917-5.02330.14311470.12232827X-RAY DIFFRACTION99
5.0233-26.04880.16321680.15482970X-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)
11.0079-0.08730.15472.08050.31021.47890.00170.009-0.15380.01920.0002-0.22920.08980.11430.00240.1620.0156-0.00320.17420.00350.18684.408517.2856-9.9449
21.6023-0.64160.33061.8641-0.53381.1552-0.01450.04630.14570.11750.0464-0.2134-0.11280.0407-0.04320.202-0.0238-0.0080.17770.01870.18790.954540.5381-10.8067
31.7621-0.334-0.55951.88770.49651.6718-0.08750.1037-0.3235-0.0454-0.02290.26320.176-0.19420.080.2211-0.02810.03980.1972-0.07810.2716-15.10326.564-17.7686
41.8899-0.21150.51062.45850.14581.7823-0.01120.4089-0.1147-0.176-0.08660.4851-0.0155-0.2320.07170.1986-0.0116-0.0060.3763-0.0760.3296-30.838723.1024-23.4636
52.40360.6914-0.09552.3203-0.1421.2814-0.02310.21810.293-0.12010.09170.3164-0.1557-0.1987-0.0490.21540.02660.00980.22880.07120.2553-21.046244.3087-19.0937
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 1:150
2X-RAY DIFFRACTION2chain B and resid 1:150
3X-RAY DIFFRACTION3chain C and resid 1:150
4X-RAY DIFFRACTION4chain D and resid 1:150
5X-RAY DIFFRACTION5chain E and resid 1:150

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