[English] 日本語
Yorodumi
- PDB-4ae1: Crystal structure of diphtheria toxin mutant CRM197 in complex wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ae1
TitleCrystal structure of diphtheria toxin mutant CRM197 in complex with nicotinamide
ComponentsDIPHTHERIA TOXIN
KeywordsTOXIN
Function / homology
Function and homology information


NAD+-diphthamide ADP-ribosyltransferase / NAD+-diphthamide ADP-ribosyltransferase activity / Uptake and function of diphtheria toxin / protein transmembrane transporter activity / nucleotidyltransferase activity / toxin activity / extracellular space / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Diphtheria toxin, translocation domain / Diphtheria toxin, receptor-binding domain / Diphtheria toxin, receptor-binding domain / Diphtheria toxin, receptor-binding domain superfamily / Diphtheria toxin, R domain / Diphtheria toxin (NAD+-dipthamide ADP-ribosyltransferase) / Diphtheria toxin, catalytic domain / Diphtheria toxin, C domain / Diphtheria toxin, translocation domain superfamily / Diphtheria toxin, T domain ...Diphtheria toxin, translocation domain / Diphtheria toxin, receptor-binding domain / Diphtheria toxin, receptor-binding domain / Diphtheria toxin, receptor-binding domain superfamily / Diphtheria toxin, R domain / Diphtheria toxin (NAD+-dipthamide ADP-ribosyltransferase) / Diphtheria toxin, catalytic domain / Diphtheria toxin, C domain / Diphtheria toxin, translocation domain superfamily / Diphtheria toxin, T domain / Diphtheria Toxin; domain 1 / Diphtheria Toxin, domain 1 / Globin-like / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE / Diphtheria toxin
Similarity search - Component
Biological speciesCORYNEBACTERIUM DIPHTHERIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.078 Å
AuthorsMalito, E. / Spraggon, G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural Basis for Lack of Toxicity of the Diphtheria Toxin Mutant Crm197.
Authors: Malito, E. / Bursulaya, B. / Chen, C. / Surdo, P.L. / Picchianti, M. / Balducci, E. / Biancucci, M. / Brock, A. / Berti, F. / Bottomley, M.J. / Nissum, M. / Costantino, P. / Rappuoli, R. / Spraggon, G.
History
DepositionJan 4, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Other
Revision 1.2Dec 20, 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_sheet / 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_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DIPHTHERIA TOXIN
B: DIPHTHERIA TOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,2114
Polymers116,9672
Non-polymers2442
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7720 Å2
ΔGint-20.9 kcal/mol
Surface area40180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.650, 69.260, 69.680
Angle α, β, γ (deg.)98.36, 99.57, 97.76
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein DIPHTHERIA TOXIN / / DT / NAD(+)--DIPHTHAMIDE ADP-RIBOSYLTRANSFERASE / DIPHTHERIA TOXIN FRAGMENT A / DIPHTHERIA TOXIN ...DT / NAD(+)--DIPHTHAMIDE ADP-RIBOSYLTRANSFERASE / DIPHTHERIA TOXIN FRAGMENT A / DIPHTHERIA TOXIN FRAGMENT B / CRM197


Mass: 58483.422 Da / Num. of mol.: 2 / Mutation: YES / Source method: isolated from a natural source / Source: (natural) CORYNEBACTERIUM DIPHTHERIAE (bacteria)
References: UniProt: P00588, NAD+-diphthamide ADP-ribosyltransferase
#2: Chemical ChemComp-NCA / NICOTINAMIDE / Nicotinamide


Mass: 122.125 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H6N2O / Comment: medication*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLY 53 TO GLU ENGINEERED RESIDUE IN CHAIN B, GLY 53 TO GLU
Sequence detailsCOORDINATES USE STANDARD RESIDUE NUMBERING FOR CONSISTENCY WITH PREVIOUS WORK RESULTING IN THE ...COORDINATES USE STANDARD RESIDUE NUMBERING FOR CONSISTENCY WITH PREVIOUS WORK RESULTING IN THE NATURAL GLY TO GLU MUTATION AT POSITION 52 INSTEAD OF 53. RESIDUES 1-32 IN THE UNIPROT SEQUENCE ARE THE SIGNAL PEPTIDE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57 % / Description: NONE
Crystal growpH: 9 / Details: 1.9 M AMMONIUM SULFATE, 100 MM BICINE [PH 9.0]

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 7, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.08→52.5 Å / Num. obs: 64344 / % possible obs: 90.3 % / Observed criterion σ(I): 1 / Redundancy: 1.9 % / Biso Wilson estimate: 29.89 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 8.8
Reflection shellResolution: 2.08→2.19 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.4 / % possible all: 84.8

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SGK

1sgk


Resolution: 2.078→52.561 Å / SU ML: 0.34 / σ(F): 0.01 / Phase error: 26.05 / Stereochemistry target values: ML
Details: RESIDUES OF CHAIN A 38-50, 188-199, 350-353, 502-503, AND 517-519, ARE DISORDERED. AND RESIDUES OF CHAIN B 1-3, 38-50, 188-200, 352-353 AND 517-520, ARE DISORDERED. DISORDERED SIDE CHAINS ...Details: RESIDUES OF CHAIN A 38-50, 188-199, 350-353, 502-503, AND 517-519, ARE DISORDERED. AND RESIDUES OF CHAIN B 1-3, 38-50, 188-200, 352-353 AND 517-520, ARE DISORDERED. DISORDERED SIDE CHAINS WERE MODELED UP TO THE BACKBONE BETA ATOMS, AND RESIDUE NAMES WERE KEPT CONSISTENT WITH WITH THE SEQUENCE OF THE PROTEIN.
RfactorNum. reflection% reflection
Rfree0.2439 3019 5.1 %
Rwork0.1955 --
obs0.198 59591 83.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.156 Å2 / ksol: 0.367 e/Å3
Displacement parametersBiso mean: 40 Å2
Baniso -1Baniso -2Baniso -3
1--1.7665 Å20.1379 Å20.4956 Å2
2--4.0574 Å2-0.1731 Å2
3----2.2909 Å2
Refinement stepCycle: LAST / Resolution: 2.078→52.561 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7446 0 18 252 7716
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077627
X-RAY DIFFRACTIONf_angle_d1.05910371
X-RAY DIFFRACTIONf_dihedral_angle_d13.572657
X-RAY DIFFRACTIONf_chiral_restr0.0711198
X-RAY DIFFRACTIONf_plane_restr0.0051356
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.078-2.15230.32812660.26294630X-RAY DIFFRACTION68
2.1523-2.23850.31772470.25564829X-RAY DIFFRACTION71
2.2385-2.34040.31722820.23315188X-RAY DIFFRACTION77
2.3404-2.46370.2642640.21245513X-RAY DIFFRACTION81
2.4637-2.61810.28023070.20095743X-RAY DIFFRACTION85
2.6181-2.82020.23563200.19345912X-RAY DIFFRACTION88
2.8202-3.1040.23723310.19186081X-RAY DIFFRACTION90
3.104-3.55310.23263480.18366162X-RAY DIFFRACTION92
3.5531-4.47610.21083280.15696214X-RAY DIFFRACTION92
4.4761-52.57770.21543260.18646300X-RAY DIFFRACTION93
Refinement TLS params.Method: refined / Origin x: 1.349 Å / Origin y: -48.4499 Å / Origin z: 30.4154 Å
111213212223313233
T0.0964 Å20.001 Å20.0214 Å2-0.0594 Å2-0.0067 Å2--0.0447 Å2
L0.9647 °2-0.2986 °20.1738 °2-0.6633 °2-0.0917 °2--0.6882 °2
S0.0983 Å °0.0712 Å °-0.026 Å °-0.0537 Å °-0.0818 Å °0.0734 Å °0.027 Å °0.0876 Å °-0.0171 Å °
Refinement TLS groupSelection details: ALL

+
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