[English] 日本語
Yorodumi
- PDB-1bi3: STRUCTURE OF APO-AND HOLO-DIPHTHERIA TOXIN REPRESSOR -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1bi3
TitleSTRUCTURE OF APO-AND HOLO-DIPHTHERIA TOXIN REPRESSOR
ComponentsDIPHTHERIA TOXIN REPRESSOR
KeywordsREPRESSOR / TRANSCRIPTION REGULATION / DNA-BINDING / IRON
Function / homology
Function and homology information


transition metal ion binding / SH3 domain binding / protein dimerization activity / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA binding / identical protein binding / cytoplasm
Similarity search - Function
Diphteria toxin repressor, SH3 domain / Diphteria toxin repressor SH3 domain / Ferrous iron transport protein A (FeoA) / Iron dependent repressor, metal binding and dimerisation domain / Ferrous iron transporter, core domain / Ferrous iron transporter FeoA domain / FeoA / : / DtxR-type HTH domain profile. / DTXR-type HTH domain ...Diphteria toxin repressor, SH3 domain / Diphteria toxin repressor SH3 domain / Ferrous iron transport protein A (FeoA) / Iron dependent repressor, metal binding and dimerisation domain / Ferrous iron transporter, core domain / Ferrous iron transporter FeoA domain / FeoA / : / DtxR-type HTH domain profile. / DTXR-type HTH domain / Iron dependent repressor, N-terminal DNA binding domain / Iron dependent repressor, metal binding and dimerisation domain / Iron dependent repressor / Iron dependent repressor, metal binding and dimerisation domain superfamily / Iron dependent repressor, metal binding and dimerisation domain / Helix-turn-helix diphteria tox regulatory element / Diphtheria Toxin Repressor; domain 2 / Transcriptional repressor, C-terminal / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / SH3 type barrels. / Arc Repressor Mutant, subunit A / Roll / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Diphtheria toxin repressor / Diphtheria toxin repressor
Similarity search - Component
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPohl, E. / Hol, W.G.J.
Citation
Journal: J.Biol.Chem. / Year: 1998
Title: Motion of the DNA-binding domain with respect to the core of the diphtheria toxin repressor (DtxR) revealed in the crystal structures of apo- and holo-DtxR.
Authors: Pohl, E. / Holmes, R.K. / Hol, W.G.
#1: Journal: Structure / Year: 1995
Title: Three-Dimensional Structure of the Diphtheria Toxin Repressor in Complex with Divalent Cation Co-Repressors
Authors: Qiu, X. / Verlinde, C.L. / Zhang, S. / Schmitt, M.P. / Holmes, R.K. / Hol, W.G.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1992
Title: Purification and Characterization of the Diphtheria Toxin Repressor
Authors: Schmitt, M.P. / Twiddy, E.M. / Holmes, R.K.
History
DepositionJun 21, 1998Processing site: BNL
Revision 1.0Jun 22, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / struct_conn / 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 / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)51,0876
Polymers50,7642
Non-polymers3234
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-136 kcal/mol
Surface area16540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.400, 63.400, 213.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein DIPHTHERIA TOXIN REPRESSOR / DTXR


Mass: 25381.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Strain: C7(-) / Gene: DTXR / Plasmid: PMS298 / Gene (production host): T / Production host: Escherichia coli (E. coli) / Strain (production host): DH5-ALPHA / References: UniProt: P33120, UniProt: P0DJL7*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 57 %
Crystal growpH: 8.5 / Details: pH 8.5
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop / Details: Qiu, X., (1995) Structure (London), 3, 87.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
13 mg/mlprotein1drop
20.5 mM1dropCoCl2
350 mMTris-HCl1droppH8.0
41.0 Mammonium sulfate1drop
520 mM2-mercaptoethanol1drop
61.8-2.0 Mammonium sulfate1reservoir
710 mM1reservoirZn2+

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Type: NSLS / Wavelength: 1.28
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1997 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28 Å / Relative weight: 1
ReflectionResolution: 2.4→8 Å / Num. obs: 19014 / % possible obs: 96 % / Observed criterion σ(I): 2 / Redundancy: 9 % / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 17
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.178 / Mean I/σ(I) obs: 7.2 / Rsym value: 0.178 / % possible all: 91
Reflection
*PLUS
Num. measured all: 177437
Reflection shell
*PLUS
% possible obs: 91 %

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→8 Å / Cross valid method: R-FREE / σ(F): 2
Details: 2FO-FC ELECTRON DENSITY IS MISSING FOR RESIDUES 1 - 3, 141 - 147 AND 199 - 200. THESE RESIDUES ARE ASSUMED TO BE DISORDERED. THE EXPERIMENTAL ELECTRON DENSITY IS WEAK OR MISSING FOR RESIDUES 148 - 226.
RfactorNum. reflection% reflectionSelection details
Rfree0.333 1205 5 %RANDOM
Rwork0.253 ---
obs0.253 19014 95.8 %-
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2670 0 12 169 2851
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.44
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg20.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.16

+
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