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- PDB-2axu: Structure of PrgX -

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Basic information

Entry
Database: PDB / ID: 2axu
TitleStructure of PrgX
ComponentsPrgX
KeywordsTRANSCRIPTION / Repressor / pheromone / DNA binding
Function / homology
Function and homology information


transcription repressor complex / negative regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Pheromone cCF10 receptor, C-terminal TPR region / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #400 / 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 ...Pheromone cCF10 receptor, C-terminal TPR region / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #400 / 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
Helix-turn-helix domain-containing protein
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / ISO to Y153C / Resolution: 2.9 Å
AuthorsShi, K. / Brown, C.K. / Gu, Z.Y. / Kozlowicz, B.K. / Dunny, G.M. / Ohlendorf, D.H. / Earhart, C.A.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: Structure of peptide sex pheromone receptor PrgX and PrgX/pheromone complexes and regulation of conjugation in Enterococcus faecalis.
Authors: Shi, K. / Brown, C.K. / Gu, Z.Y. / Kozlowicz, B.K. / Dunny, G.M. / Ohlendorf, D.H. / Earhart, C.A.
History
DepositionSep 6, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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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: PrgX
F: PrgX
G: PrgX
H: PrgX
I: PrgX
J: PrgX
K: PrgX
L: PrgX


Theoretical massNumber of molelcules
Total (without water)448,46412
Polymers448,46412
Non-polymers00
Water6,918384
1
A: PrgX
B: PrgX
E: PrgX
F: PrgX


Theoretical massNumber of molelcules
Total (without water)149,4884
Polymers149,4884
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13050 Å2
ΔGint-66 kcal/mol
Surface area53250 Å2
MethodPISA
2
C: PrgX
D: PrgX
K: PrgX
L: PrgX


Theoretical massNumber of molelcules
Total (without water)149,4884
Polymers149,4884
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12920 Å2
ΔGint-63 kcal/mol
Surface area52860 Å2
MethodPISA
3
G: PrgX
H: PrgX
I: PrgX
J: PrgX


Theoretical massNumber of molelcules
Total (without water)149,4884
Polymers149,4884
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12900 Å2
ΔGint-63 kcal/mol
Surface area53230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.654, 134.718, 195.930
Angle α, β, γ (deg.)90.00, 100.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
PrgX


Mass: 37372.016 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q04114
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG 4000, citrate-phophate , pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorDetector: CCD / Date: Mar 3, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.9→15 Å / Num. all: 104010 / Num. obs: 104010 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: ISO to Y153C / Resolution: 2.9→15 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.266 5265 RANDOM
Rwork0.199 --
all0.201 104010 -
obs0.201 104010 -
Refinement stepCycle: LAST / Resolution: 2.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29763 0 0 384 30147

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