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- PDB-1g3s: CYS102SER DTXR -

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Basic information

Entry
Database: PDB / ID: 1g3s
TitleCYS102SER DTXR
ComponentsDIPHTHERIA TOXIN REPRESSOR
KeywordsGENE REGULATION / DNA binding protein / iron dependent regulator
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 / Winged helix DNA-binding domain superfamily / Roll / 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 / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPohl, E. / Goranson-Siekierke, J. / Holmes, R.K. / Hol, W.G.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Structures of three diphtheria toxin repressor (DtxR) variants with decreased repressor activity.
Authors: Pohl, E. / Goranson-Siekierke, J. / Choi, M.K. / Roosild, T. / Holmes, R.K. / Hol, W.G.
History
DepositionOct 25, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_sheet
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_sheet.number_strands
Revision 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DIPHTHERIA TOXIN REPRESSOR


Theoretical massNumber of molelcules
Total (without water)25,3341
Polymers25,3341
Non-polymers00
Water1,44180
1
A: DIPHTHERIA TOXIN REPRESSOR

A: DIPHTHERIA TOXIN REPRESSOR


Theoretical massNumber of molelcules
Total (without water)50,6672
Polymers50,6672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Unit cell
Length a, b, c (Å)63.6, 63.6, 110.3
Angle α, β, γ (deg.)90, 90, 120
Int Tables number152
Space group name H-MP3121
DetailsThe biologiocal active unit is a dimer

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Components

#1: Protein DIPHTHERIA TOXIN REPRESSOR / DTXR


Mass: 25333.730 Da / Num. of mol.: 1 / Mutation: C102S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P33120, UniProt: P0DJL7*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5
Details: Ammonium sulfate, EDTA, glycerol, pH 8.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Nov 12, 1996 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→99 Å / Num. all: 10663 / Num. obs: 10070 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 49 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 20.8
Reflection shellResolution: 2.4→2.48 Å / Redundancy: 6 % / Rmerge(I) obs: 0.429 / % possible all: 95.2

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→8 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.271 295 random
Rwork0.185 --
all-9980 -
obs-9704 -
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1949 0 0 240 2189
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.7

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