[English] 日本語
Yorodumi
- PDB-2c8f: Structure of the ARTT motif E214N mutant C3bot1 Exoenzyme (NAD-bo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2c8f
TitleStructure of the ARTT motif E214N mutant C3bot1 Exoenzyme (NAD-bound state, crystal form III)
ComponentsMONO-ADP-RIBOSYLTRANSFERASE C3
KeywordsTRANSFERASE / C3 EXOENZYME / ARTT MOTIF / BACTERIAL TOXINS / GLYCOSYLTRANSFERASE
Function / homology
Function and homology information


NAD+-protein mono-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / nucleotidyltransferase activity / extracellular region
Similarity search - Function
Mono-ADP-ribosyltransferase C3/Edin / Toxin ADP-ribosyltransferase; Chain A, domain 1 / Toxin ADP-ribosyltransferase; Chain A, domain 1 / ADP ribosyltransferase / ADP-ribosyltransferase exoenzyme / Toxin-related mono-ADP-ribosyltransferase (TR mART) core domain profile. / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Mono-ADP-ribosyltransferase C3 / Exoenzyme C3
Similarity search - Component
Biological speciesCLOSTRIDIUM BOTULINUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsStura, E.A. / Menetrey, J. / Flatau, G. / Boquet, P. / Menez, A.
Citation
Journal: Protein Sci. / Year: 2008
Title: Structural Basis for the Nad-Hydrolysis Mechanism and the Artt-Loop Plasticity of C3 Exoenzymes.
Authors: Menetrey, J. / Flatau, G. / Boquet, P. / Menez, A. / Stura, E.A.
#1: Journal: J.Biol.Chem. / Year: 2002
Title: Nad Binding Induces Conformational Changes in Rho Adp-Ribosylating Clostridium Botulinum C3 Exoenzyme.
Authors: Menetrey, J. / Flatau, G. / Stura, E.A. / Charbonnier, J.B. / Gas, F. / Teulon, J.M. / Ledu, M.H. / Boquet, P. / Menez, A.
History
DepositionDec 3, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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
E: MONO-ADP-RIBOSYLTRANSFERASE C3
F: MONO-ADP-RIBOSYLTRANSFERASE C3
G: MONO-ADP-RIBOSYLTRANSFERASE C3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3944
Polymers70,7313
Non-polymers6631
Water54030
1
E: MONO-ADP-RIBOSYLTRANSFERASE C3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2402
Polymers23,5771
Non-polymers6631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
F: MONO-ADP-RIBOSYLTRANSFERASE C3


Theoretical massNumber of molelcules
Total (without water)23,5771
Polymers23,5771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
G: MONO-ADP-RIBOSYLTRANSFERASE C3


Theoretical massNumber of molelcules
Total (without water)23,5771
Polymers23,5771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.837, 70.381, 114.688
Angle α, β, γ (deg.)90.00, 97.28, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein MONO-ADP-RIBOSYLTRANSFERASE C3 / EXOENZYME C3


Mass: 23576.957 Da / Num. of mol.: 3 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM BOTULINUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: P15879, UniProt: Q7M0L1*PLUS, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 53.8 %
Crystal growDetails: 22.5% PEG 3350 W/W, 100 MM LI2SO4, 100 MM SODIUM CITRATE PH 3.0, 3-10% MPEG 550 V/V

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.933
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.5→29.88 Å / Num. obs: 22416 / % possible obs: 90.8 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.9

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GZF

1gzf


Resolution: 2.5→29.88 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.878 / SU B: 13.831 / SU ML: 0.306 / Cross valid method: THROUGHOUT / ESU R: 0.885 / ESU R Free: 0.381 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.316 1145 5.1 %RANDOM
Rwork0.232 ---
obs0.237 21244 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 46.46 Å2
Baniso -1Baniso -2Baniso -3
1-7.42 Å20 Å21.5 Å2
2---2.4 Å20 Å2
3----4.64 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4704 0 44 30 4778
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224835
X-RAY DIFFRACTIONr_bond_other_d0.0020.024316
X-RAY DIFFRACTIONr_angle_refined_deg1.561.9666513
X-RAY DIFFRACTIONr_angle_other_deg0.855310112
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5965601
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0840.2719
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025318
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02944
X-RAY DIFFRACTIONr_nbd_refined0.2160.2980
X-RAY DIFFRACTIONr_nbd_other0.2330.24638
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0870.22727
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.281
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1210.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.150.218
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2280.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7261.52992
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.3524791
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.75431843
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9164.51722
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.494 73
Rwork0.331 1319

+
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