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- PDB-4hiz: Phage phi92 endosialidase -

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Basic information

Entry
Database: PDB / ID: 4hiz
TitlePhage phi92 endosialidase
ComponentsEndosialidase
KeywordsHYDROLASE / VIRAL PROTEIN / sialidase fold / beta-helix / endo-alpha2 / 8-sialidase / 9-sialidase / Sialic acid polymer
Function / homology
Function and homology information


endo-alpha-sialidase / endo-alpha-(2,8)-sialidase activity / virus tail / metal ion binding
Similarity search - Function
Endosialidase, N-terminal extension domain / Endosialidase, domain 4 / Endosialidase, domain 4 / Glycosyl hydrolase 58 / Endosialidase, beta barrel domain / Endosialidase, beta propeller domain / Endosialidase, N-terminal extension domain / Endosialidase, C-terminal domain / Beta barrel domain of bacteriophage endosialidase / Catalytic beta propeller domain of bacteriophage endosialidase ...Endosialidase, N-terminal extension domain / Endosialidase, domain 4 / Endosialidase, domain 4 / Glycosyl hydrolase 58 / Endosialidase, beta barrel domain / Endosialidase, beta propeller domain / Endosialidase, N-terminal extension domain / Endosialidase, C-terminal domain / Beta barrel domain of bacteriophage endosialidase / Catalytic beta propeller domain of bacteriophage endosialidase / N terminal extension of bacteriophage endosialidase / Catalytic domain of bacteriophage endosialidase / Endosialidase, C-terminal domain superfamily / Intramolecular chaperone auto-processing domain / Chaperone of endosialidase / Intramolecular chaperone auto-processing (ICA) domain profile. / Transcription Regulator spoIIAA / Elongation Factor Tu (Ef-tu); domain 3 - #20 / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / ATP synthase subunit alpha, N-terminal domain-like superfamily / Elongation Factor Tu (Ef-tu); domain 3 / Few Secondary Structures / Irregular / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
sucrose / Phi92_gp143
Similarity search - Component
Biological speciesEnterobacteria phage phi92 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.601 Å
AuthorsSchwarzer, D. / Browning, C. / Leiman, P.G.
CitationJournal: Virology / Year: 2015
Title: Structure and biochemical characterization of bacteriophage phi92 endosialidase.
Authors: Schwarzer, D. / Browning, C. / Stummeyer, K. / Oberbeck, A. / Muhlenhoff, M. / Gerardy-Schahn, R. / Leiman, P.G.
History
DepositionOct 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / 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 / _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.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 28, 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
Revision 2.2Apr 16, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endosialidase
B: Endosialidase
C: Endosialidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,19676
Polymers227,9923
Non-polymers6,20473
Water63,0343499
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41410 Å2
ΔGint-199 kcal/mol
Surface area62840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.858, 137.584, 140.778
Angle α, β, γ (deg.)90.00, 94.64, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2023-

HOH

21B-1598-

HOH

31B-1606-

HOH

41B-1835-

HOH

51C-1874-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Endosialidase / Phi92_gp143


Mass: 75997.320 Da / Num. of mol.: 3 / Fragment: UNP residues 76-756
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage phi92 (virus) / Strain: ATCC 35860-B1 / Gene: gene 143, PHI92_gene_143 / Plasmid: pET22b-Strep / Production host: Escherichia coli (E. coli) / Strain (production host): E.coli BL21-Gold(DE3) / References: UniProt: I7HXG2, endo-alpha-sialidase

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Sugars , 2 types, 6 molecules

#2: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-9)-N-acetyl-beta-neuraminic acid


Type: oligosaccharide / Mass: 600.525 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-9DNeup5Acb2-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[Aad21122h-2b_2-6_5*NCC/3=O][Aad21122h-2a_2-6_5*NCC/3=O]/1-2/a9-b2WURCSPDB2Glycan 1.1.0
[][b-D-Neup5Ac]{[(9+2)][a-D-Neup5Ac]{}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 6 types, 3566 molecules

#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 43 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#8: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Na
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3499 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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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: 2.6 Å3/Da / Density % sol: 52.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 6% PEG 3350 70 mM CHES pH 9.5 70 mM Strontium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 7, 2010 / Details: Mirrors
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→91.52 Å / Num. obs: 305050 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.042 / Rsym value: 0.058 / Net I/σ(I): 17.1
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 4.3 / Rsym value: 0.362 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
AMoREphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
SCALEPACKdata scaling
RemDAqdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.601→19.968 Å / Cor.coef. Fo:Fc: 0.989 / Cor.coef. Fo:Fc free: 0.975 / SU ML: 0.12 / σ(F): 0.2 / Phase error: 15.79 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.1468 3113 1.02 %
Rwork0.107 --
obs0.1074 304531 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.573 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0.06 Å2
2--0.04 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.601→19.968 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15517 0 388 3499 19404
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01416755
X-RAY DIFFRACTIONf_angle_d1.52322860
X-RAY DIFFRACTIONf_dihedral_angle_d17.2496164
X-RAY DIFFRACTIONf_chiral_restr0.1662442
X-RAY DIFFRACTIONf_plane_restr0.0072922
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6011-1.62610.22491420.157313446X-RAY DIFFRACTION98
1.6261-1.65270.19661390.148913648X-RAY DIFFRACTION100
1.6527-1.68120.191420.142313675X-RAY DIFFRACTION100
1.6812-1.71180.21041480.135713695X-RAY DIFFRACTION100
1.7118-1.74470.16941510.123713651X-RAY DIFFRACTION100
1.7447-1.78030.1621310.117113706X-RAY DIFFRACTION100
1.7803-1.81890.15541110.11213697X-RAY DIFFRACTION100
1.8189-1.86120.16841400.1113648X-RAY DIFFRACTION100
1.8612-1.90770.14961500.107613692X-RAY DIFFRACTION100
1.9077-1.95930.14821430.099213752X-RAY DIFFRACTION100
1.9593-2.01690.14531570.097813619X-RAY DIFFRACTION100
2.0169-2.08190.13851520.092713690X-RAY DIFFRACTION100
2.0819-2.15620.13661510.092213741X-RAY DIFFRACTION100
2.1562-2.24240.14041800.09313645X-RAY DIFFRACTION100
2.2424-2.34440.13641440.096913692X-RAY DIFFRACTION100
2.3444-2.46770.15751380.100113719X-RAY DIFFRACTION100
2.4677-2.6220.15751350.10313739X-RAY DIFFRACTION100
2.622-2.8240.14511210.105213740X-RAY DIFFRACTION100
2.824-3.10720.16371330.110413739X-RAY DIFFRACTION100
3.1072-3.55460.12791610.101913761X-RAY DIFFRACTION100
3.5546-4.47020.10121200.091613802X-RAY DIFFRACTION100
4.4702-19.96950.14851240.124613921X-RAY DIFFRACTION100

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