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- PDB-2awi: Structure of PrgX Y153C mutant -

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Basic information

Entry
Database: PDB / ID: 2awi
TitleStructure of PrgX Y153C mutant
ComponentsPrgX
KeywordsTRANSCRIPTION / Repressor / pheromone / DNA binding / regulatory domain
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 / SYNCHROTRON / MAD / Resolution: 2.25 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 1, 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
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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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)447,18112
Polymers447,18112
Non-polymers00
Water11,674648
1
A: PrgX
B: PrgX
E: PrgX
F: PrgX


Theoretical massNumber of molelcules
Total (without water)149,0604
Polymers149,0604
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13360 Å2
ΔGint-64 kcal/mol
Surface area52450 Å2
MethodPISA
2
C: PrgX
D: PrgX
K: PrgX
L: PrgX


Theoretical massNumber of molelcules
Total (without water)149,0604
Polymers149,0604
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13060 Å2
ΔGint-61 kcal/mol
Surface area52560 Å2
MethodPISA
3
G: PrgX
H: PrgX
I: PrgX
J: PrgX


Theoretical massNumber of molelcules
Total (without water)149,0604
Polymers149,0604
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13070 Å2
ΔGint-63 kcal/mol
Surface area52810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.527, 134.366, 195.199
Angle α, β, γ (deg.)90.00, 100.28, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
PrgX


Mass: 37265.090 Da / Num. of mol.: 12 / Mutation: Y153C
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 / Water


Mass: 18.015 Da / Num. of mol.: 648 / 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: 2.6 Å3/Da / Density % sol: 52.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5
Details: PEG 4000, citrate-phophate, pH 5.0, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.97926, 0.97945, 0.97772
DetectorDetector: CCD / Date: Mar 3, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979261
20.979451
30.977721
ReflectionResolution: 2.25→29.9 Å / Num. obs: 212720

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT1.7data extraction
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.25→29.9 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.271 8055 5 %RANDOM
Rwork0.218 ---
all0.221 159184 --
obs0.221 212720 98.6 %-
Solvent computationBsol: 40.141 Å2
Displacement parametersBiso mean: 51.967 Å2
Baniso -1Baniso -2Baniso -3
1--11.285 Å2-0 Å2-6.247 Å2
2---0.688 Å2-0 Å2
3---11.973 Å2
Refinement stepCycle: LAST / Resolution: 2.25→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29388 0 0 648 30036
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param

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