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- PDB-2grl: Crystal structure of dCT/iCF10 complex -

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Basic information

Entry
Database: PDB / ID: 2grl
TitleCrystal structure of dCT/iCF10 complex
Components
  • PrgX
  • peptide
KeywordsTRANSCRIPTION / receptor / inhibitor
Function / homology
Function and homology information


transcription repressor complex / negative regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #400 / HTH-type transcriptional regulator Rgg, C-terminal domain / Transcription activator MutR, C-terminal / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / lambda repressor-like DNA-binding domains / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat ...Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #400 / HTH-type transcriptional regulator Rgg, C-terminal domain / Transcription activator MutR, C-terminal / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / lambda repressor-like DNA-binding domains / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Pheromone cCF10 receptor
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsShi, K. / Kozlowicz, B.K. / Gu, Z.Y. / Ohlendorf, D.H. / Earhart, C.A. / Dunny, G.M.
CitationJournal: Mol.Microbiol. / Year: 2006
Title: Molecular basis for control of conjugation by bacterial pheromone and inhibitor peptides.
Authors: Kozlowicz, B.K. / Shi, K. / Gu, Z.Y. / Ohlendorf, D.H. / Earhart, C.A. / Dunny, G.M.
History
DepositionApr 24, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: PrgX
B: PrgX
C: PrgX
D: PrgX
E: peptide


Theoretical massNumber of molelcules
Total (without water)149,3405
Polymers149,3405
Non-polymers00
Water82946
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.750, 110.124, 188.599
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is the tetramer in the assymetric unit.

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Components

#1: Protein
PrgX


Mass: 37137.547 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Production host: Escherichia coli (E. coli) / References: GenBank: 150553, UniProt: Q04114*PLUS
#2: Protein/peptide peptide /


Mass: 790.002 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.91 Å3/Da / Density % sol: 57.75 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 5.6 / Details: LiCl, pH 5.6, EVAPORATION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 1, 2005
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→40 Å / Num. all: 35934 / Num. obs: 35826 / % possible obs: 99.7 % / Observed criterion σ(I): 2
Reflection shellResolution: 3→3.11 Å / % possible all: 97.8

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Processing

Software
NameVersionClassification
CrystalCleardata collection
d*TREKdata reduction
EPMRphasing
CNS1.1refinement
CrystalClear(MSC/RIGAKU)data reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→40 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.271 1784 random
Rwork0.238 --
all0.246 35535 -
obs0.238 35535 -
Refinement stepCycle: LAST / Resolution: 3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9510 0 0 46 9556
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.1
X-RAY DIFFRACTIONc_dihedral_angle_d18.1
X-RAY DIFFRACTIONc_improper_angle_d0.78

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