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Basic information

Entry
Database: PDB / ID: 5jsd
TitleCrystal structure of phiAB6 tailspike in complex with five-repeated oligosaccharides of Acinetobacter baumannii surface polysaccharide
ComponentsphiAB6 tailspike
KeywordsVIRAL PROTEIN / viral tailspike / beta-helix / superhelical trimer
Function / homology
Function and homology information


symbiont entry into host cell via disruption of host cell glycocalyx / symbiont entry into host cell via disruption of host cell envelope / virus tail / virion attachment to host cell
Similarity search - Function
Pectate lyase superfamily protein / Pectate lyase superfamily protein / Pectin lyase fold / Pectin lyase fold/virulence factor
Similarity search - Domain/homology
ACETIC ACID / MALONIC ACID / Tail fiber
Similarity search - Component
Biological speciesunidentified phage (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsLee, I.M. / Tu, I.F. / Huang, K.F. / Wu, S.H.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology and Academia SinicaNSC101-2923-B-001-005-MY3, MOST104-2325-B-001-003, NSC-101-2319-B-001-003, and MOST105-0210-01-12-01 Taiwan
CitationJournal: Sci Rep / Year: 2017
Title: Structural basis for fragmenting the exopolysaccharide of Acinetobacter baumannii by bacteriophage Phi AB6 tailspike protein
Authors: Lee, I.M. / Tu, I.F. / Yang, F.L. / Ko, T.P. / Liao, J.H. / Lin, N.T. / Wu, C.Y. / Ren, C.T. / Wang, A.H. / Chang, C.M. / Huang, K.F. / Wu, S.H.
History
DepositionMay 8, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 2.0Nov 29, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / pdbx_distant_solvent_atoms / pdbx_struct_assembly_gen / pdbx_validate_close_contact / refine / refine_ls_shell / reflns / 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.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _pdbx_distant_solvent_atoms.auth_asym_id / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_distant_solvent_atoms.neighbor_ligand_distance / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _pdbx_struct_assembly_gen.asym_id_list / _refine.B_iso_mean / _refine.aniso_B[1][2] / _refine.aniso_B[2][3] / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_percent_reflns_obs / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _reflns.d_resolution_low
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_struct_special_symmetry / pdbx_validate_close_contact / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _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_comp_id_1 / _pdbx_validate_close_contact.auth_comp_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Mar 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / 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: phiAB6 tailspike
B: phiAB6 tailspike
C: phiAB6 tailspike
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,67124
Polymers235,2703
Non-polymers8,40121
Water51,9372883
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area45620 Å2
ΔGint-38 kcal/mol
Surface area51830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.805, 78.393, 247.738
Angle α, β, γ (deg.)90.00, 100.53, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-1554-

HOH

21B-1644-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein phiAB6 tailspike


Mass: 78423.227 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified phage (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A159BDB5*PLUS

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Sugars , 2 types, 6 molecules

#2: Polysaccharide beta-D-galactopyranose-(1-3)-2-amino-2-deoxy-beta-D-galactopyranose-(1-3)-[5,7-bisacetamido-3,5,7,9- ...beta-D-galactopyranose-(1-3)-2-amino-2-deoxy-beta-D-galactopyranose-(1-3)-[5,7-bisacetamido-3,5,7,9-tetradeoxy-L-glycero-alpha-L-manno-non-2-ulopyranosonic acid-(2-6)-beta-D-glucopyranose-(1-6)]beta-D-galactopyranose-(1-3)-2-amino-2-deoxy-beta-D-galactopyranose-(1-3)-[beta-D-glucopyranose-(1-6)]beta-D-galactopyranose


Type: oligosaccharide / Mass: 1467.338 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/4,8,7/[a2112h-1b_1-5][a2112h-1b_1-5_2*N][a2122h-1b_1-5][Aad22111m-2a_2-6_5*NCC/3=O_7*NCC/3=O]/1-2-1-2-1-3-4-3/a3-b1_a6-h1_b3-c1_c3-d1_c6-f1_d3-e1_f6-g2WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+1)][b-D-GalpN]{[(3+1)][b-D-Galp]{[(3+1)][b-D-GalpN]{[(3+1)][b-D-Galp]{}}[(6+1)][b-D-Glcp]{[(6+2)]{}}}}[(6+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-glucopyranose-(1-6)-beta-D-galactopyranose-(1-3)-2-amino-2-deoxy-beta-D-galactopyranose-(1-3) ...beta-D-glucopyranose-(1-6)-beta-D-galactopyranose-(1-3)-2-amino-2-deoxy-beta-D-galactopyranose-(1-3)-[beta-D-glucopyranose-(1-6)]beta-D-galactopyranose-(1-3)-2-amino-2-deoxy-beta-D-galactopyranose


Type: oligosaccharide / Mass: 988.890 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-6DGalpb1-3DGalpNb1-3[DGlcpb1-6]DGalpb1-3DGalpNb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2112h-1b_1-5_2*N][a2112h-1b_1-5][a2122h-1b_1-5]/1-2-1-2-3-3/a3-b1_b3-c1_b6-f1_c3-d1_d6-e1WURCSPDB2Glycan 1.1.0
[][b-D-GalpN]{[(3+1)][b-D-Galp]{[(3+1)][b-D-GalpN]{[(3+1)][b-D-Galp]{[(6+1)][b-D-Glcp]{}}}[(6+1)][b-D-Glcp]{}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 2898 molecules

#4: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H4O4
#5: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H4O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2883 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsAUTHORS STATE THAT THE DNA AND PROTEIN SEQUENCES HAVE BEEN DEPOSITED IN GENBACK WITH A ACCESSION ...AUTHORS STATE THAT THE DNA AND PROTEIN SEQUENCES HAVE BEEN DEPOSITED IN GENBACK WITH A ACCESSION NUMBER OF KT339321.

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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: 2.76 Å3/Da / Density % sol: 55.36 % / Description: rhombus-shaped
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1.0 M sodium malonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Apr 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.48→20 Å / Num. obs: 399721 / % possible obs: 94.1 % / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 20.8
Reflection shellResolution: 1.48→1.53 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 2 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→19.77 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.187 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.169 18826 5 %RANDOM
Rwork0.142 ---
obs0.144 354372 87.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.89 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.01 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.48→19.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12564 0 558 2883 16005
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0213451
X-RAY DIFFRACTIONr_bond_other_d0.0030.0212213
X-RAY DIFFRACTIONr_angle_refined_deg1.3311.97218282
X-RAY DIFFRACTIONr_angle_other_deg1.041328089
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.54151647
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.0824.767579
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.826152007
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4671545
X-RAY DIFFRACTIONr_chiral_restr0.0730.22145
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215138
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023171
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5821.4026597
X-RAY DIFFRACTIONr_mcbond_other0.5771.46589
X-RAY DIFFRACTIONr_mcangle_it0.6712.1028220
X-RAY DIFFRACTIONr_mcangle_other0.6712.1028221
X-RAY DIFFRACTIONr_scbond_it0.8691.6616854
X-RAY DIFFRACTIONr_scbond_other0.8711.6616855
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.8942.6310059
X-RAY DIFFRACTIONr_long_range_B_refined2.73815.09818230
X-RAY DIFFRACTIONr_long_range_B_other2.54614.56517624
X-RAY DIFFRACTIONr_rigid_bond_restr1.626325574
X-RAY DIFFRACTIONr_sphericity_free22.7065685
X-RAY DIFFRACTIONr_sphericity_bonded5.228527458
LS refinement shellResolution: 1.48→1.52 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.224 734 -
Rwork0.211 13721 -
obs--46.67 %

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