[English] 日本語
Yorodumi
- PDB-7ee4: Crystal structure of Neu5Ac bound PltC -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ee4
TitleCrystal structure of Neu5Ac bound PltC
ComponentsSubtilase cytotoxin subunit B-like protein
KeywordsTOXIN / typhoid toxin
Function / homologyEnterotoxin / N-acetyl-alpha-neuraminic acid / Subtilase cytotoxin subunit B-like protein
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Typhi str. CT18 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsLiu, X.Y. / Chen, Z. / Gao, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770143 China
CitationJournal: Mbio / Year: 2022
Title: Molecular Insights into the Assembly and Functional Diversification of Typhoid Toxin.
Authors: Liu, X. / Chen, Z. / Jiao, X. / Jiang, X. / Qiu, J. / You, F. / Long, H. / Cao, H. / Fowler, C.C. / Gao, X.
History
DepositionMar 17, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Subtilase cytotoxin subunit B-like protein
B: Subtilase cytotoxin subunit B-like protein
C: Subtilase cytotoxin subunit B-like protein
D: Subtilase cytotoxin subunit B-like protein
E: Subtilase cytotoxin subunit B-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,72811
Polymers69,2925
Non-polymers2,4366
Water11,962664
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)189.447, 189.447, 41.526
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
d_1ens_1
d_2ens_1
d_3ens_1
d_4ens_1
d_5ens_1

NCS oper:
IDCodeMatrixVector
1given(0.465476209138, -0.788485785423, 0.402022468168), (0.87172990389, 0.329899880118, -0.362288619421), (0.15303226258, 0.51909174072, 0.840907183538)-28.8759679623, -25.8525037525, 18.8246149427
2given(-0.397587797466, 0.600962707078, 0.693374190469), (-0.39119278916, -0.794569537125, 0.464357031155), (0.829995268068, -0.0866202942462, 0.551003429761)23.8444107171, -66.6108776177, -4.18913353061
3given(-0.374185284913, -0.414974512458, 0.829325947119), (0.636823213846, -0.765073205047, -0.0954944251069), (0.674122812892, 0.492401406304, 0.550544537897)-13.7811685406, -66.2006436235, 17.5393518804
4given(0.470052125526, 0.865271510915, 0.174230340893), (-0.80072732972, 0.334993290579, 0.49660370388), (0.371331041968, -0.372940622172, 0.850310854691)32.920222135, -23.9730703385, -14.610712676

-
Components

-
Protein , 1 types, 5 molecules ABCDE

#1: Protein
Subtilase cytotoxin subunit B-like protein / PltB homolog protein


Mass: 13858.360 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhi str. CT18 (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A716TY65

-
Sugars , 3 types, 4 molecules

#2: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 633.552 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1a_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a4-b1_b3-c2WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#3: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 471.411 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2/a3-b2WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}LINUCSPDB-CARE
#5: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H19NO9 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 2 types, 666 molecules

#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.: 664 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 34% PEG500MME and 0.1M sodium citrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.4→29.18 Å / Num. obs: 109189 / % possible obs: 99.72 % / Redundancy: 4.5 % / Biso Wilson estimate: 11.15 Å2 / CC1/2: 0.995 / Rrim(I) all: 0.07 / Net I/σ(I): 43.53
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 3.4 % / Num. unique obs: 10912 / CC1/2: 0.848 / Rrim(I) all: 0.382

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WHT

5wht


Resolution: 1.4→29.18 Å / SU ML: 0.1076 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 17.5091
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1718 5455 5 %
Rwork0.151 103604 -
obs0.152 109059 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.39 Å2
Refinement stepCycle: LAST / Resolution: 1.4→29.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4666 0 165 664 5495
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01884960
X-RAY DIFFRACTIONf_angle_d1.74816715
X-RAY DIFFRACTIONf_chiral_restr0.1329742
X-RAY DIFFRACTIONf_plane_restr0.0116837
X-RAY DIFFRACTIONf_dihedral_angle_d16.48511714
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.21661840.19273438X-RAY DIFFRACTION98.64
1.42-1.430.21122100.18863473X-RAY DIFFRACTION99.7
1.43-1.450.19841670.17883415X-RAY DIFFRACTION99.8
1.45-1.470.21131820.17493459X-RAY DIFFRACTION99.81
1.47-1.490.20511870.16813504X-RAY DIFFRACTION99.81
1.49-1.510.18781680.15763407X-RAY DIFFRACTION99.55
1.51-1.530.19331620.16313491X-RAY DIFFRACTION99.67
1.53-1.550.19312060.15523447X-RAY DIFFRACTION99.89
1.55-1.580.22571820.15683488X-RAY DIFFRACTION99.86
1.58-1.60.20431760.15173457X-RAY DIFFRACTION99.92
1.6-1.630.16261740.15133444X-RAY DIFFRACTION99.92
1.63-1.660.18482050.15273500X-RAY DIFFRACTION99.73
1.66-1.690.18531990.15383361X-RAY DIFFRACTION99.55
1.69-1.730.17341970.15873498X-RAY DIFFRACTION99.89
1.73-1.760.1661830.15413428X-RAY DIFFRACTION99.89
1.76-1.80.19091780.15133504X-RAY DIFFRACTION99.73
1.8-1.850.1641740.15513435X-RAY DIFFRACTION99.83
1.85-1.90.18891770.15293484X-RAY DIFFRACTION99.65
1.9-1.960.16311570.14693432X-RAY DIFFRACTION99.45
1.96-2.020.18091920.14763460X-RAY DIFFRACTION99.92
2.02-2.090.16861780.14813485X-RAY DIFFRACTION99.81
2.09-2.170.16871650.14773444X-RAY DIFFRACTION99.56
2.17-2.270.17941730.15273444X-RAY DIFFRACTION98.99
2.27-2.390.17721960.15393467X-RAY DIFFRACTION99.73
2.39-2.540.18211770.16353438X-RAY DIFFRACTION99.78
2.54-2.740.1761710.16413466X-RAY DIFFRACTION99.64
2.74-3.010.1561610.16083428X-RAY DIFFRACTION98.52
3.02-3.450.17051820.14793476X-RAY DIFFRACTION99.65
3.45-4.340.13741910.12293418X-RAY DIFFRACTION99.31
4.35-29.180.15522010.13743413X-RAY DIFFRACTION98.93

+
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