[English] 日本語
Yorodumi
- PDB-3ki4: Catalytic fragment of Cholix toxin from Vibrio Cholerae in comple... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ki4
TitleCatalytic fragment of Cholix toxin from Vibrio Cholerae in complex with inhibitor GP-P
ComponentsCholix toxin
KeywordsTransferase / toxin / ADP-ribosyl transferase / alpha-beta complex / diphthamide
Function / homology
Function and homology information


NAD+-diphthamide ADP-ribosyltransferase / NAD+-diphthamide ADP-ribosyltransferase activity / nucleotidyltransferase activity / toxin activity
Similarity search - Function
Exotoxin A catalytic domain / Exotoxin A, binding / Exotoxin A, middle domain / Exotoxin A, middle domain superfamily / Exotoxin A catalytic / Exotoxin A binding / Exotoxin A, targeting / Diphtheria Toxin; domain 1 / Diphtheria Toxin, domain 1 / Concanavalin A-like lectin/glucanase domain superfamily ...Exotoxin A catalytic domain / Exotoxin A, binding / Exotoxin A, middle domain / Exotoxin A, middle domain superfamily / Exotoxin A catalytic / Exotoxin A binding / Exotoxin A, targeting / Diphtheria Toxin; domain 1 / Diphtheria Toxin, domain 1 / Concanavalin A-like lectin/glucanase domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-G9P / Cholix toxin
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsJorgensen, R. / Edwards, P.R. / Merrill, A.R.
CitationJournal: To be Published
Title: Structure function analysis of soluble inhibitors of cholix toxin from Vibrio cholerae
Authors: Jorgensen, R. / Edwards, P.R. / Merrill, A.R.
History
DepositionOct 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Cholix toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8364
Polymers23,3351
Non-polymers5023
Water4,774265
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.525, 64.685, 84.226
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Cholix toxin


Mass: 23334.842 Da / Num. of mol.: 1 / Fragment: catalytic domain, residues 459-665
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: TP / Gene: chxa, toxA / Plasmid: pET28+ / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566
References: UniProt: Q5EK40, NAD+-diphthamide ADP-ribosyltransferase
#2: Chemical ChemComp-G9P / (11bR)-3-oxo-1,2,3,11b-tetrahydrochromeno[4,3,2-de]isoquinoline-10-sulfonic acid / 1,11b-Dihydro-[1]benzopyrano[4,3,2-de]isoquinolin-3(2H)-one-10-sulphonic acid


Mass: 317.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H11NO5S
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsCOMPOUND G9P IS NAMED COMPOUND P8 IN THE PRIMARY CITATION

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 5% PEG-8000, 0.02 M KH2PO4, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97934 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 23, 2008
RadiationMonochromator: White beam slits, cryo-cooled first and sagittally bent second crystal of double crystal monochromator (DCM), vertically focusing mirror (VFM)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.65→30 Å / Num. obs: 22167 / % possible obs: 92.3 % / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 15.36 Å2 / Rmerge(I) obs: 0.1 / Χ2: 1.02 / Net I/σ(I): 8.7
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 3.5 / Num. unique all: 1538 / Χ2: 0.844 / % possible all: 65.4

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.8 Å22.03 Å
Translation1.8 Å22.03 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
MXData Collectiondata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Q6M

2q6m


Resolution: 1.65→22.03 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.872 / SU B: 3.686 / SU ML: 0.067 / Isotropic thermal model: Isotropic with 10 TLS groups / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.202 1142 5.2 %RANDOM
Rwork0.167 ---
obs0.169 22125 92.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 52.74 Å2 / Biso mean: 13.225 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.65→22.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1552 0 34 265 1851
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0211640
X-RAY DIFFRACTIONr_angle_refined_deg1.4071.9562240
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7965201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.1324.12580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.10815247
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.9511511
X-RAY DIFFRACTIONr_chiral_restr0.1040.2242
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021283
X-RAY DIFFRACTIONr_nbd_refined0.2030.2738
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21144
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2202
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1140.225
X-RAY DIFFRACTIONr_mcbond_it0.7971.51025
X-RAY DIFFRACTIONr_mcangle_it1.21621608
X-RAY DIFFRACTIONr_scbond_it2.2833710
X-RAY DIFFRACTIONr_scangle_it3.5144.5631
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 64 -
Rwork0.226 999 -
all-1063 -
obs--61.27 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
111.7525-7.6574-2.451822.44417.59484.05890.05630.19390.4679-0.37380.2292-0.65150.03220.1945-0.2855-0.01720.00550.03270.01240.01280.10961.87511.413-18.967
22.5765-0.9416-0.50435.2735-1.87882.47680.02640.1841-0.12-0.23790.0105-0.16710.00380.0144-0.03690.0395-0.01170.02410.055-0.00510.05651.147-0.642-22.51
31.4775-0.10590.31321.7671-0.33430.1216-0.0326-0.04880.03650.01090.0015-0.03240.0120.0450.03110.0450.00320.00470.05680.00580.0569-4.8332.382-11.927
412.5643.3403-7.21051.4441-1.72274.72260.4452-0.43461.18520.31610.00490.1761-0.24580.2316-0.450.1245-0.02090.04140.0527-0.02270.0846-12.3526.5611.798
50.07040.218-0.4630.8479-0.76785.5940.05220.00330.09930.01630.09750.08020.0485-0.1943-0.14980.0455-0.00650.00520.07340.00340.0476-17.8481.587-8.996
60.3374-0.63030.05653.9255-0.15780.2125-0.02590.00540.0230.21450.0174-0.0426-0.0148-0.05130.00840.050.001-0.00160.05310.00430.0639-13.59219.383-14.347
71.45740.08430.51591.59810.08680.6568-0.0796-0.0756-0.15820.030.0314-0.11650.0362-0.01910.04820.04870.00990.00430.05980.02430.0443-11.705-10.158-7.09
83.48711.07721.60131.5099-0.34523.50650.1184-0.3371-0.03660.1717-0.01230.1213-0.0824-0.2947-0.10610.0513-0.01250.02220.06880.00970.0024-23.988-6.8031.488
90.660.12460.10070.6643-0.14390.51270.0069-0.0366-0.00440.0183-0.00040.0034-0.0189-0.008-0.00650.03460.00460.00250.0571-0.00260.0372-13.9982.245-12.906
102.67362.24-4.26133.4687-3.62516.7937-0.20570.1916-0.0994-0.13130.2447-0.0030.2316-0.2751-0.03910.0479-0.0138-0.00960.05970.00340.0668-13.106-9.063-16.919
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A423 - 435
2X-RAY DIFFRACTION2A436 - 449
3X-RAY DIFFRACTION3A450 - 471
4X-RAY DIFFRACTION4A472 - 487
5X-RAY DIFFRACTION5A488 - 500
6X-RAY DIFFRACTION6A501 - 530
7X-RAY DIFFRACTION7A531 - 545
8X-RAY DIFFRACTION8A546 - 565
9X-RAY DIFFRACTION9A566 - 616
10X-RAY DIFFRACTION10A617 - 628

+
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