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Basic information

Entry
Database: PDB / ID: 6vt2
TitleSialic acid binding region of Streptococcus sanguinis SK1 adhesin bound to sTa
ComponentsAdhesin
KeywordsCELL ADHESION / bacterial adhesion / adhesin / serine rich repeat / streptococcus
Function / homologyImmunoglobulin-like - #4140 / Ubiquitin-like (UB roll) - #890 / Ubiquitin-like (UB roll) / Roll / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Function and homology information
Biological speciesStreptococcus sanguinis SK1 = NCTC 7863 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsStubbs, H.E. / Iverson, T.M.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5T32GM008320-28 United States
National Institutes of Health/National Eye Institute (NIH/NEI)5T32EY007135-24 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI106987 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI10400 United States
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)DE019807 United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Tandem sialoglycan-binding modules in a Streptococcus sanguinis serine-rich repeat adhesin create target dependent avidity effects.
Authors: Stubbs, H.E. / Bensing, B.A. / Yamakawa, I. / Sharma, P. / Yu, H. / Chen, X. / Sullam, P.M. / Iverson, T.M.
History
DepositionFeb 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 2.0Mar 10, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / citation_author / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_distant_solvent_atoms / pdbx_entity_instance_feature / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_struct_special_symmetry / pdbx_validate_chiral / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_symm_contact / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct / struct_conf / struct_conn
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 / _entity.pdbx_number_of_molecules / _entity.src_method / _pdbx_branch_scheme.pdb_asym_id / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_distant_solvent_atoms.neighbor_ligand_distance / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _pdbx_refine_tls.L[1][1] / _pdbx_refine_tls.L[1][2] / _pdbx_refine_tls.L[1][3] / _pdbx_refine_tls.L[2][2] / _pdbx_refine_tls.L[2][3] / _pdbx_refine_tls.L[3][3] / _pdbx_refine_tls.S[1][1] / _pdbx_refine_tls.S[1][2] / _pdbx_refine_tls.S[1][3] / _pdbx_refine_tls.S[2][1] / _pdbx_refine_tls.S[2][2] / _pdbx_refine_tls.S[2][3] / _pdbx_refine_tls.S[3][1] / _pdbx_refine_tls.S[3][2] / _pdbx_refine_tls.S[3][3] / _pdbx_refine_tls.T[1][1] / _pdbx_refine_tls.T[1][2] / _pdbx_refine_tls.T[1][3] / _pdbx_refine_tls.T[2][2] / _pdbx_refine_tls.T[2][3] / _pdbx_refine_tls.T[3][3] / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_refine_tls_group.beg_auth_asym_id / _pdbx_refine_tls_group.beg_auth_seq_id / _pdbx_refine_tls_group.beg_label_asym_id / _pdbx_refine_tls_group.beg_label_seq_id / _pdbx_refine_tls_group.end_auth_asym_id / _pdbx_refine_tls_group.end_auth_seq_id / _pdbx_refine_tls_group.end_label_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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_struct_special_symmetry.auth_seq_id / _refine.B_iso_mean / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_ls_restr.dev_ideal / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.percent_reflns_obs / _struct.title / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_length / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id
Description: Chirality error / Provider: author / Type: Coordinate replacement
Revision 2.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adhesin
E: Adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,50720
Polymers88,9152
Non-polymers3,59118
Water29,4001632
1
A: Adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1599
Polymers44,4581
Non-polymers1,7028
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,34711
Polymers44,4581
Non-polymers1,89010
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.213, 269.859, 47.511
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+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-705-

SO4

21A-1334-

HOH

31E-2023-

HOH

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Components

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Protein / Sugars , 2 types, 6 molecules AE

#1: Protein Adhesin


Mass: 44457.645 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sanguinis SK1 = NCTC 7863 (bacteria)
Strain: SK1 / Production host: Escherichia coli (E. coli)
#2: Polysaccharide
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose


Type: oligosaccharide / Mass: 674.604 Da / Num. of mol.: 4 / Source method: obtained synthetically
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-3DGalpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2112h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a3-b1_b3-c2WURCSPDB2Glycan 1.1.0
[][a-D-GalpNAc]{[(3+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 1646 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1632 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.96 Å3/Da / Density % sol: 58.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: Protein concentration: 72 mg/mL, Protein buffer: 150 mM NaCl, 20 mM tris pH 7.6, Reservoir solution: 20% (w/v) PEG 3350, 0.2 M MgSO4, 0.01 M SrCl2. Crystals were soaked with 10 mM sTa and ...Details: Protein concentration: 72 mg/mL, Protein buffer: 150 mM NaCl, 20 mM tris pH 7.6, Reservoir solution: 20% (w/v) PEG 3350, 0.2 M MgSO4, 0.01 M SrCl2. Crystals were soaked with 10 mM sTa and cryoprotected with 40% (1:1 ethylene glycol: glycerol) and 60% reservoir solution

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97946 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Dec 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.52→50 Å / Num. obs: 148960 / % possible obs: 93.1 % / Redundancy: 4.3 % / Biso Wilson estimate: 14.52 Å2 / Rsym value: 0.067 / Net I/σ(I): 26.6
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 2.8 % / Num. unique obs: 9822 / CC1/2: 0.723 / % possible all: 61

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874+SVNrefinement
Cootmodel building
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6VS7

6vs7


Resolution: 1.52→35.66 Å / SU ML: 0.1703 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.8784
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.193 7361 4.96 %
Rwork0.177 141139 -
obs0.1778 148500 91.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.83 Å2
Refinement stepCycle: LAST / Resolution: 1.52→35.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6271 0 163 1692 8126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02166744
X-RAY DIFFRACTIONf_angle_d1.63499269
X-RAY DIFFRACTIONf_chiral_restr0.09741102
X-RAY DIFFRACTIONf_plane_restr0.01191228
X-RAY DIFFRACTIONf_dihedral_angle_d20.79852479
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.52-1.540.2888780.26141532X-RAY DIFFRACTION30.14
1.54-1.560.32572000.25913831X-RAY DIFFRACTION75.33
1.56-1.580.26832080.24133973X-RAY DIFFRACTION77.84
1.58-1.60.2662200.22634230X-RAY DIFFRACTION82.88
1.6-1.620.22862320.21624462X-RAY DIFFRACTION87.95
1.62-1.640.24652450.20624700X-RAY DIFFRACTION90.95
1.64-1.660.23512580.20434922X-RAY DIFFRACTION96.89
1.66-1.690.22712620.19375048X-RAY DIFFRACTION99.42
1.69-1.710.19822670.18585116X-RAY DIFFRACTION99.54
1.71-1.740.21882640.18555052X-RAY DIFFRACTION99.61
1.74-1.770.21962670.18185119X-RAY DIFFRACTION99.52
1.77-1.810.21762630.17545066X-RAY DIFFRACTION99.42
1.81-1.840.20442670.18445102X-RAY DIFFRACTION99.37
1.84-1.880.20972630.25063X-RAY DIFFRACTION98.83
1.88-1.920.39932450.37894756X-RAY DIFFRACTION92.49
1.92-1.960.19662650.18355071X-RAY DIFFRACTION98.67
1.96-2.010.18072670.16675091X-RAY DIFFRACTION99.61
2.01-2.070.18442700.16335186X-RAY DIFFRACTION99.6
2.07-2.130.17442640.1595065X-RAY DIFFRACTION99.53
2.13-2.20.16682660.15795102X-RAY DIFFRACTION98.84
2.2-2.270.2182990.17022028X-RAY DIFFRACTION39.08
2.27-2.370.17072680.15655122X-RAY DIFFRACTION99.12
2.37-2.470.17122320.15965172X-RAY DIFFRACTION99.76
2.47-2.60.1972620.16675136X-RAY DIFFRACTION99.48
2.6-2.770.17632730.16425167X-RAY DIFFRACTION99.13
2.77-2.980.17282770.16195170X-RAY DIFFRACTION98.64
2.98-3.280.17152830.16455176X-RAY DIFFRACTION99.56
3.28-3.750.17292070.15623960X-RAY DIFFRACTION74.99
3.75-4.730.1442710.1425260X-RAY DIFFRACTION98.28
4.73-35.660.19353180.18295461X-RAY DIFFRACTION98.79
Refinement TLS params.Method: refined / Origin x: 83.0439347566 Å / Origin y: 72.130781572 Å / Origin z: -0.0373834230536 Å
111213212223313233
T0.110012642626 Å2-0.000338913415708 Å2-0.0262859924413 Å2-0.115885065317 Å20.000844570496594 Å2--0.108619937122 Å2
L0.00340118704233 °20.00269750276627 °2-0.0391509996525 °2-0.155968583924 °20.000578681324869 °2---0.0122779123531 °2
S0.0033901086868 Å °0.00162839842766 Å °0.00724743188164 Å °-0.00198660724297 Å °-0.00277566515303 Å °0.00347640598827 Å °-0.00369246642227 Å °-0.00167820080857 Å °-0.000291960449813 Å °
Refinement TLS groupSelection details: all

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