[English] 日本語
Yorodumi
- PDB-3tew: Crystal Structure of Anthrax Protective Antigen (Membrane Inserti... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3tew
TitleCrystal Structure of Anthrax Protective Antigen (Membrane Insertion Loop Deleted) to 1.45-A resolution
ComponentsProtective antigen
Keywordsprotein transport / toxin
Function / homology
Function and homology information


symbiont-mediated suppression of host MAPK cascade / host cell cytosol / Uptake and function of anthrax toxins / host cell endosome membrane / protein homooligomerization / toxin activity / host cell plasma membrane / extracellular region / metal ion binding / identical protein binding / membrane
Similarity search - Function
Toxin - Anthrax Protective Antigen; domain 1 / Toxin - Anthrax Protective Antigen;domain 1 / Immunoglobulin-like - #810 / Ubiquitin-like (UB roll) - #110 / Protective antigen, heptamerisation domain / Protective antigen domain 4 / : / Anthrax protective antigen, immunoglobulin-like domain / PA14/GLEYA domain / PA14 domain profile. ...Toxin - Anthrax Protective Antigen; domain 1 / Toxin - Anthrax Protective Antigen;domain 1 / Immunoglobulin-like - #810 / Ubiquitin-like (UB roll) - #110 / Protective antigen, heptamerisation domain / Protective antigen domain 4 / : / Anthrax protective antigen, immunoglobulin-like domain / PA14/GLEYA domain / PA14 domain profile. / Bacterial exotoxin B / Protective antigen, heptamerisation domain / Protective antigen, Ca-binding domain / Clostridial binary toxin B/anthrax toxin PA, domain 3 / Protective antigen, heptamerisation domain superfamily / Clostridial binary toxin B/anthrax toxin PA Ca-binding domain / Clostridial binary toxin B/anthrax toxin PA domain 2 / Clostridial binary toxin B/anthrax toxin PA domain 3 / PA14 domain / PA14 / PA14 domain / Ubiquitin-like (UB roll) / Jelly Rolls / Roll / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
2-METHOXYETHANOL / Protective antigen
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsFeld, G.K. / Krantz, B.A.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Domain flexibility modulates the heterogeneous assembly mechanism of anthrax toxin protective antigen.
Authors: Feld, G.K. / Kintzer, A.F. / Tang, I.I. / Thoren, K.L. / Krantz, B.A.
History
DepositionAug 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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 / _struct_conn.pdbx_dist_value / _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.ptnr1_label_seq_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protective antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,0426
Polymers80,7341
Non-polymers3085
Water6,269348
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.355, 93.385, 118.078
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Protective antigen / PA / Anthrax toxins translocating protein / PA-83 / PA83 / Protective antigen PA-20 / PA20 / ...PA / Anthrax toxins translocating protein / PA-83 / PA83 / Protective antigen PA-20 / PA20 / Protective antigen PA-63 / PA63


Mass: 80733.641 Da / Num. of mol.: 1 / Mutation: V303P,H304G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: BXA0164, GBAA_pXO1_0164, pag, pagA, PX01, pXO1-110 / Plasmid: pET22b+ / Production host: Escherichia coli (E. coli) / Strain (production host): DE3(BL21) / References: UniProt: P13423*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MXE / 2-METHOXYETHANOL


Mass: 76.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CLOSEST DATABASE REFERENCE TO THE CRYSTALLIZED SEQUENCE CORRESPONDS TO UNP ENTRY P13423, WHICH ...THE CLOSEST DATABASE REFERENCE TO THE CRYSTALLIZED SEQUENCE CORRESPONDS TO UNP ENTRY P13423, WHICH CONTAINS A PRESEQUENCE THAT IS NOT INCLUDED IN NATURAL ANTHRAX PA, NOR WAS A PART OF THE PROTEIN CRYSTALLIZED. THE RESIDUE NUMBERS IN THIS STRUCTURE CONFORM TO THE SEQUENCE FOR PDB ACCESSION CODE 1ACC. TO CLARIFY IN TERMS OF UNP SEQUENCE, THE MUTATIONS MADE WERE V332P AND H333G.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.52 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% PEG-ME 2000, 0.1M Tris-Cl, 0.2M Trimethylamine-N-oxide, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 7, 2009
RadiationMonochromator: Synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 1.45→23 Å / Num. all: 126263 / Num. obs: 126263 / % possible obs: 90.3 % / Observed criterion σ(F): 1.9 / Observed criterion σ(I): 1.9 / Redundancy: 6.5 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Net I/σ(I): 13.9
Reflection shellResolution: 1.45→1.49 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.748 / Mean I/σ(I) obs: 1.9 / Num. unique all: 7983 / Rsym value: 0.748 / % possible all: 81

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ACC

1acc


Resolution: 1.45→23 Å / SU ML: 0.19 / σ(F): 0.06 / Phase error: 22.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2163 2000 1.58 %Random
Rwork0.1935 ---
obs0.1938 126247 90.26 %-
all-126263 --
Solvent computationShrinkage radii: 1.37 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.323 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.6285 Å20 Å20 Å2
2--8.3831 Å20 Å2
3---34.0534 Å2
Refinement stepCycle: LAST / Resolution: 1.45→23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5568 0 17 348 5933
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085775
X-RAY DIFFRACTIONf_angle_d1.1517849
X-RAY DIFFRACTIONf_dihedral_angle_d11.7332213
X-RAY DIFFRACTIONf_chiral_restr0.08890
X-RAY DIFFRACTIONf_plane_restr0.0051028
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4501-1.48640.33211260.29817857X-RAY DIFFRACTION81
1.4864-1.52660.32751320.26668139X-RAY DIFFRACTION84
1.5266-1.57150.28581330.23958333X-RAY DIFFRACTION86
1.5715-1.62220.2431330.20688271X-RAY DIFFRACTION85
1.6222-1.68010.20561300.17997998X-RAY DIFFRACTION82
1.6801-1.74740.21241310.17458177X-RAY DIFFRACTION84
1.7474-1.82690.19561350.15178421X-RAY DIFFRACTION86
1.8269-1.92320.18421420.14318792X-RAY DIFFRACTION90
1.9232-2.04360.17761490.14239239X-RAY DIFFRACTION94
2.0436-2.20130.18571550.15649598X-RAY DIFFRACTION98
2.2013-2.42260.17821540.17589620X-RAY DIFFRACTION97
2.4226-2.77260.21611570.21529707X-RAY DIFFRACTION98
2.7726-3.49120.26091580.20219887X-RAY DIFFRACTION99
3.4912-23.00630.21151650.202110208X-RAY DIFFRACTION99

+
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