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- PDB-8f9r: Rabbit sialic acid esterase (SIAE) -

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Basic information

Entry
Database: PDB / ID: 8f9r
TitleRabbit sialic acid esterase (SIAE)
ComponentsSialic acid acetylesterase
KeywordsHYDROLASE / sialic acid / sialate o-acetylesterase
Function / homologySialate O-acetylesterase / Sialate O-acetylesterase domain / Carbohydrate esterase, sialic acid-specific acetylesterase / sialate O-acetylesterase activity / SGNH hydrolase superfamily / carbohydrate metabolic process / Sialic acid acetylesterase
Function and homology information
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.97 Å
AuthorsIde, D. / Gorelik, A. / Illes, K. / Nagar, B.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)250057 Canada
CitationJournal: J.Mol.Biol. / Year: 2024
Title: Structural Analysis of Mammalian Sialic Acid Esterase.
Authors: Ide, D. / Gorelik, A. / Illes, K. / Nagar, B.
History
DepositionNov 24, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2024Provider: repository / Type: Initial release
Revision 2.0Sep 11, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / entity ...atom_site / entity / pdbx_branch_scheme / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_restr_ncs / refine_ls_shell / struct_asym / struct_conn / struct_mon_prot_cis / struct_ncs_dom / struct_ncs_dom_lim / struct_ncs_oper
Item: _pdbx_entity_nonpoly.entity_id / _pdbx_nonpoly_scheme.auth_seq_num ..._pdbx_entity_nonpoly.entity_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_validate_torsion.auth_asym_id / _pdbx_validate_torsion.auth_comp_id / _pdbx_validate_torsion.auth_seq_id / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_restr_ncs.pdbx_asym_id / _refine_ls_restr_ncs.rms_dev_position / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _struct_asym.entity_id / _struct_mon_prot_cis.pdbx_omega_angle / _struct_ncs_dom.details
Description: Atomic clashes / Provider: author / Type: Coordinate replacement
Revision 2.1Oct 23, 2024Group: Database references / Structure summary
Category: citation / pdbx_entry_details / pdbx_modification_feature
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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sialic acid acetylesterase
B: Sialic acid acetylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,46914
Polymers114,2482
Non-polymers8,22212
Water1629
1
A: Sialic acid acetylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2357
Polymers57,1241
Non-polymers4,1116
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sialic acid acetylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2357
Polymers57,1241
Non-polymers4,1116
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.070, 152.690, 81.748
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11LYSLYSILEILEAA22 - 5119 - 498
d_12NAGNAGNAGNAGAM601
d_13NAGNAGNAGNAGCC1
d_14NAGNAGNAGNAGCC2
d_15BMABMABMABMACC3
d_16MANMANMANMANCC4
d_17MANMANMANMANCC5
d_18NAGNAGNAGNAGDD1
d_19NAGNAGNAGNAGDD2
d_110NAGNAGNAGNAGEE1
d_111NAGNAGNAGNAGEE2
d_112BMABMABMABMAEE3
d_113MANMANMANMANEE4
d_114NAGNAGNAGNAGFF1
d_115NAGNAGNAGNAGFF2
d_116BMABMABMABMAFF3
d_117MANMANMANMANFF4
d_118MANMANMANMANFF5
d_119NAGNAGNAGNAGGG1
d_120NAGNAGNAGNAGGG2
d_121FUCFUCFUCFUCDD4
d_122MANMANMANMANEE5
d_123BMABMABMABMADD3
d_21LYSLYSILEILEBB22 - 5119 - 498
d_22NAGNAGNAGNAGBN601
d_23NAGNAGNAGNAGHH1
d_24NAGNAGNAGNAGHH2
d_25BMABMABMABMAHH3
d_26MANMANMANMANHH4
d_27MANMANMANMANHH5
d_28NAGNAGNAGNAGII1
d_29NAGNAGNAGNAGII2
d_210NAGNAGNAGNAGJJ1
d_211NAGNAGNAGNAGJJ2
d_212BMABMABMABMAJJ3
d_213MANMANMANMANJJ4
d_214NAGNAGNAGNAGKK1
d_215NAGNAGNAGNAGKK2
d_216BMABMABMABMAKK3
d_217MANMANMANMANKK4
d_218MANMANMANMANKK5
d_219NAGNAGNAGNAGLL1
d_220NAGNAGNAGNAGLL2
d_221FUCFUCFUCFUCII4
d_222MANMANMANMANJJ5
d_223BMABMABMABMAII3

NCS oper: (Code: givenMatrix: (0.988331107627, -0.0289932975631, -0.149535983605), (-0.0291009676052, -0.999575398435, 0.00146851220759), (-0.149515067404, 0.002900265518, -0.988755193705)Vector: -5. ...NCS oper: (Code: given
Matrix: (0.988331107627, -0.0289932975631, -0.149535983605), (-0.0291009676052, -0.999575398435, 0.00146851220759), (-0.149515067404, 0.002900265518, -0.988755193705)
Vector: -5.67451514793, 66.8230719792, -5.30395985195)

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Components

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Protein / Non-polymers , 2 types, 11 molecules AB

#1: Protein Sialic acid acetylesterase


Mass: 57123.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: SIAE / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A5F9D0N0
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 4 types, 12 molecules

#2: Polysaccharide
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

Has ligand of interestN
Has protein modificationY

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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: 3.12 Å3/Da / Density % sol: 60.52 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium phosphate, 0.1 M Tris, pH 8.5, 50% v/v MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 59316 / % possible obs: 100 % / Redundancy: 11.6 % / Biso Wilson estimate: 61.56 Å2 / Rrim(I) all: 0.184 / Net I/σ(I): 14.3
Reflection shellResolution: 2.95→3.06 Å / Num. unique obs: 5810 / CC1/2: 0.314

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.97→50 Å / SU ML: 0.3057 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.4844
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2425 2941 8.57 %
Rwork0.2074 31379 -
obs0.2104 34320 60.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.94 Å2
Refinement stepCycle: LAST / Resolution: 2.97→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7838 0 548 9 8395
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048624
X-RAY DIFFRACTIONf_angle_d0.674311754
X-RAY DIFFRACTIONf_chiral_restr0.04971394
X-RAY DIFFRACTIONf_plane_restr0.00641442
X-RAY DIFFRACTIONf_dihedral_angle_d14.92753286
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.0254021081751 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.97-3.020.3638110.3802126X-RAY DIFFRACTION5.06
3.02-3.070.4432220.369230X-RAY DIFFRACTION9.43
3.07-3.130.4439310.3577320X-RAY DIFFRACTION13.2
3.13-3.190.358410.3216438X-RAY DIFFRACTION17.55
3.19-3.260.3409520.313539X-RAY DIFFRACTION21.97
3.26-3.330.3195660.3132700X-RAY DIFFRACTION28.71
3.33-3.40.2908800.3137867X-RAY DIFFRACTION34.82
3.4-3.490.34950.29751023X-RAY DIFFRACTION41.95
3.49-3.580.27371160.28281228X-RAY DIFFRACTION49.47
3.58-3.690.29461300.25361407X-RAY DIFFRACTION56.78
3.69-3.810.26761390.24321533X-RAY DIFFRACTION62.41
3.81-3.940.2491570.20441721X-RAY DIFFRACTION69.81
3.94-4.10.21551900.19441934X-RAY DIFFRACTION78.26
4.1-4.290.23341960.1862128X-RAY DIFFRACTION86.49
4.29-4.510.21862240.17032432X-RAY DIFFRACTION97.86
4.51-4.80.23632380.17332465X-RAY DIFFRACTION100
4.8-5.170.22492340.17932450X-RAY DIFFRACTION99.81
5.17-5.690.24512230.19312454X-RAY DIFFRACTION99.85
5.69-6.510.24122260.21952476X-RAY DIFFRACTION99.85
6.51-8.190.20812310.20172486X-RAY DIFFRACTION99.93
8.19-500.24062390.20442422X-RAY DIFFRACTION98.74

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