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- PDB-1igu: C-terminal Domain of the Transcriptional Repressor Protein KorB -

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Basic information

Entry
Database: PDB / ID: 1igu
TitleC-terminal Domain of the Transcriptional Repressor Protein KorB
ComponentsTranscriptional repressor protein KorB
KeywordsTRANSCRIPTION / SH3 domain / dimerization domain
Function / homology
Function and homology information


negative regulation of DNA-templated transcription / protein-containing complex / DNA binding / identical protein binding
Similarity search - Function
KorB, C-terminal domain / KorB, C-terminal / Repressor KorB domain / KorB, C-terminal domain superfamily / KorB DNA-binding domain / KorB C-terminal beta-barrel domain / KorB domain / ParB/RepB/Spo0J partition protein / ParB/Sulfiredoxin domain / ParB/Sulfiredoxin ...KorB, C-terminal domain / KorB, C-terminal / Repressor KorB domain / KorB, C-terminal domain superfamily / KorB DNA-binding domain / KorB C-terminal beta-barrel domain / KorB domain / ParB/RepB/Spo0J partition protein / ParB/Sulfiredoxin domain / ParB/Sulfiredoxin / ParB-like nuclease domain / ParB/Sulfiredoxin superfamily / Transcriptional repressor, C-terminal / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Transcriptional repressor protein KorB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDelbruck, H. / Heinemann, U.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: An Src homology 3-like domain is responsible for dimerization of the repressor protein KorB encoded by the promiscuous IncP plasmid RP4.
Authors: Delbruck, H. / Ziegelin, G. / Lanka, E. / Heinemann, U.
History
DepositionApr 18, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional repressor protein KorB
B: Transcriptional repressor protein KorB


Theoretical massNumber of molelcules
Total (without water)14,2202
Polymers14,2202
Non-polymers00
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-12 kcal/mol
Surface area6830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.680, 51.680, 87.420
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Transcriptional repressor protein KorB


Mass: 7110.020 Da / Num. of mol.: 2 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: korb / Production host: Escherichia coli (E. coli) / References: UniProt: P07674
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.37 Å3/Da / Density % sol: 48.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 4000, Na acetate, Ammonium acetate,, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 7.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris-HCl1droppH7.6
250 mM1dropNaCl
330 %PEG40001reservoir
4200 mMammonium acetate1reservoir
5100 mMsodium acetate1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 10, 1997 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→22 Å / Num. all: 7188 / Num. obs: 7157 / % possible obs: 0.99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 25.2 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 8.5
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.195 / Mean I/σ(I) obs: 3.9 / Num. unique all: 466 / % possible all: 87.9
Reflection
*PLUS
Lowest resolution: 22 Å / % possible obs: 99 %
Reflection shell
*PLUS
% possible obs: 87.9 %

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Processing

Software
NameVersionClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IGQ

1igq


Resolution: 2.2→24 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.227 735 -RANDOM
Rwork0.1517 ---
all0.1596 7157 --
obs0.1596 7157 100 %-
Displacement parametersBiso mean: 33.71 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 2.2→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms968 0 0 125 1093
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.021
X-RAY DIFFRACTIONp_angle_deg2.5283
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 24 Å / σ(F): 0 / Rfactor Rfree: 0.227
Solvent computation
*PLUS
Displacement parameters
*PLUS

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