[English] 日本語
Yorodumi
- PDB-5i4d: 1.75 Angstrom Crystal Structure of Superantigen-like Protein, Exo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5i4d
Title1.75 Angstrom Crystal Structure of Superantigen-like Protein, Exotoxin from Staphylococcus aureus, in Complex with Sialyl-LewisX.
ComponentsSuperantigen-like protein
KeywordsIMMUNE SYSTEM / Superantigen-like protein / Sialyl-LewisX / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


extracellular region
Similarity search - Function
Staphylococcus aureus exotoxin / Staphylococcal superantigen-like OB-fold domain / Staphylococcal superantigen-like OB-fold domain / Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin, conserved site / Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2. / Ubiquitin-like (UB roll) - #120 / Superantigen, staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / Superantigen toxin, C-terminal ...Staphylococcus aureus exotoxin / Staphylococcal superantigen-like OB-fold domain / Staphylococcal superantigen-like OB-fold domain / Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin, conserved site / Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2. / Ubiquitin-like (UB roll) - #120 / Superantigen, staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / Superantigen toxin, C-terminal / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / Enterotoxin / Ubiquitin-like (UB roll) / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Roll / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Sialyl-Lewis X antigen, alpha anomer / TRIETHYLENE GLYCOL / : / Staphylococcal superantigen-like 3
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsMinasov, G. / Nocadello, S. / Shuvalova, L. / Filippova, E.V. / Halavaty, A. / Dubrovska, I. / Bagnoli, F. / Falugi, F. / Bottomley, M. / Grandi, G. ...Minasov, G. / Nocadello, S. / Shuvalova, L. / Filippova, E.V. / Halavaty, A. / Dubrovska, I. / Bagnoli, F. / Falugi, F. / Bottomley, M. / Grandi, G. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 1.75 Angstrom Crystal Structure of Superantigen-like Protein, Exotoxin from Staphylococcus aureus, in Complex with Sialyl-LewisX.
Authors: Minasov, G. / Nocadello, S. / Shuvalova, L. / Filippova, E.V. / Halavaty, A. / Dubrovska, I. / Bagnoli, F. / Falugi, F. / Bottomley, M. / Grandi, G. / Anderson, W.F. / Center for Structural ...Authors: Minasov, G. / Nocadello, S. / Shuvalova, L. / Filippova, E.V. / Halavaty, A. / Dubrovska, I. / Bagnoli, F. / Falugi, F. / Bottomley, M. / Grandi, G. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionFeb 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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_prerelease_seq / pdbx_struct_assembly_gen / pdbx_struct_oper_list / 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_alt_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 / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entity_branch_descriptor / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Superantigen-like protein
B: Superantigen-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,7888
Polymers78,3872
Non-polymers2,4016
Water11,548641
1
A: Superantigen-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3594
Polymers39,1941
Non-polymers1,1653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Superantigen-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4304
Polymers39,1941
Non-polymers1,2363
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.975, 166.881, 34.144
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Superantigen-like protein


Mass: 39193.551 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: set9, ERS445052_00332, RL02_05830 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: A0A0D6GBT0, UniProt: Q2G0X7*PLUS

-
Sugars , 2 types, 3 molecules

#2: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2- ...N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-alpha-D-glucopyranose / Sialyl-Lewis X antigen / alpha anomer


Type: oligosaccharide, Oligosaccharide / Class: Antigen / Mass: 820.744 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with branches / References: Sialyl-Lewis X antigen, alpha anomer
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-4[LFucpa1-3]DGlcpNAca1-ROHGlycam Condensed SequenceGMML 1.0
[][a-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}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.: 1
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

-
Non-polymers , 3 types, 644 molecules

#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 641 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.56 Å3/Da / Density % sol: 21.27 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: Protein: 6.1 mg/ml, 0.5M Sodium chloride, 0.01M Tris-HCL (pH 8.3), 2mM Sialyl-LewisX;Screen: JCSG+ (A3), 0.18M tri-Ammonium citrate, 20% (w/v) PEG3350.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 27, 2014 / Details: C(111)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. obs: 50461 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 19.9 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 19.5
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 7 % / Rmerge(I) obs: 0.622 / Mean I/σ(I) obs: 3.1 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB-4RCO
Resolution: 1.75→29.94 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.894 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.109
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.DUE TO DEGRADATION OF THE PROTEIN DURING CRYSTALLIZATION, ONLY RESIDUES 164 TO 356 WERE OBSERVED IN THE CRYSTAL.
RfactorNum. reflection% reflectionSelection details
Rfree0.20177 2563 5.1 %RANDOM
Rwork0.16083 ---
obs0.16287 47830 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.845 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2--0.83 Å20 Å2
3----0.75 Å2
Refinement stepCycle: 1 / Resolution: 1.75→29.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3182 0 163 641 3986
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193810
X-RAY DIFFRACTIONr_bond_other_d0.0010.023757
X-RAY DIFFRACTIONr_angle_refined_deg1.5462.0165148
X-RAY DIFFRACTIONr_angle_other_deg0.81738767
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7065459
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.75125.207169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.28215773
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1441514
X-RAY DIFFRACTIONr_chiral_restr0.0980.2570
X-RAY DIFFRACTIONr_gen_planes_refined0.0220.024158
X-RAY DIFFRACTIONr_gen_planes_other0.0180.02828
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_it1.0441.3341721
X-RAY DIFFRACTIONr_mcbond_other1.0431.3341720
X-RAY DIFFRACTIONr_mcangle_it1.6761.9892194
X-RAY DIFFRACTIONr_mcangle_other1.6761.9892195
X-RAY DIFFRACTIONr_scbond_it1.6571.6382089
X-RAY DIFFRACTIONr_scbond_other1.6561.6382089
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6662.3412945
X-RAY DIFFRACTIONr_long_range_B_refined6.64413.2074671
X-RAY DIFFRACTIONr_long_range_B_other6.24911.5864281
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.752→1.798 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 198 -
Rwork0.217 3367 -
obs--96.12 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.3708-1.2006-1.08895.58554.39384.27380.12720.30430.0572-0.1911-0.0552-0.1869-0.1212-0.1322-0.07190.04480.0032-0.01910.09240.02090.045925.8714232.377-13.9666
21.1403-0.2820.38051.80580.5030.6524-0.0157-0.0802-0.0026-0.0299-0.08520.2746-0.0016-0.06520.10090.03380.00460.01140.0123-0.01880.103313.2921240.89210.921
32.9776-0.48-0.69461.27890.44751.27390.0210.11150.0168-0.03720.0466-0.002-0.0879-0.0732-0.06760.05440.00630.00510.01360.01520.068819.1418240.4718-3.3084
41.3761-1.5234-0.720610.59137.30645.13930.08490.20870.0487-0.25210.0124-0.1682-0.1530.0599-0.09730.0224-0.00880.0230.0599-0.01560.027143.5552227.042-10.0504
51.0178-0.237-0.26020.84470.1971.0837-0.01630.02010.0047-0.02130.03580.00480.00610.043-0.01950.0171-0.00980.00330.0244-0.00290.012734.0222229.011-4.9817
64.6015-1.2742-2.63941.4010.97652.2788-0.0936-0.33650.08260.23670.1423-0.06190.19390.181-0.04870.08480.0026-0.03290.03780.01120.040726.4351190.215512.2138
71.9184-0.222-0.98291.7477-0.15830.9701-0.0558-0.0544-0.2998-0.09680.0136-0.04350.0406-0.02320.04220.08940.00490.01140.0434-0.01920.144932.9033180.2322-0.6399
80.9189-1.0181-0.03622.47990.20050.3823-0.0137-0.04120.01130.21530.0699-0.137-0.00870.0415-0.05620.0512-0.0078-0.01140.0119-0.01560.044229.169194.4555.2962
910.4684-0.0996-3.43062.4558-1.22233.53770.3491-0.47090.65230.3423-0.090.1537-0.27960.1835-0.25910.1459-0.02040.05590.0275-0.03870.062817.3511213.358611.1262
100.8466-0.1288-0.20761.16630.25541.36230.0399-0.02080.00750.00750.0163-0.0096-0.0526-0.0038-0.05610.0527-0.01030.00670.0029-0.00260.027220.8003200.08134.7942
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A165 - 185
2X-RAY DIFFRACTION2A186 - 222
3X-RAY DIFFRACTION3A223 - 255
4X-RAY DIFFRACTION4A256 - 277
5X-RAY DIFFRACTION5A278 - 356
6X-RAY DIFFRACTION6B164 - 189
7X-RAY DIFFRACTION7B190 - 222
8X-RAY DIFFRACTION8B223 - 272
9X-RAY DIFFRACTION9B273 - 281
10X-RAY DIFFRACTION10B282 - 356

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more