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

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Basic information

Entry
Database: PDB / ID: 2axv
TitleStructure of PrgX Y153C mutant
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 / MOLECULAR REPLACEMENT / Resolution: 3 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
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 14, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PrgX
B: PrgX
C: PrgX
D: PrgX


Theoretical massNumber of molelcules
Total (without water)148,3104
Polymers148,3104
Non-polymers00
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13140 Å2
ΔGint-65 kcal/mol
Surface area52720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.076, 82.076, 263.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 2 / Auth seq-ID: 3 - 296 / Label seq-ID: 3 - 296

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

#1: Protein
PrgX


Mass: 37077.516 Da / Num. of mol.: 4 / 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


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.9 Å3/Da / Density % sol: 57.1 %
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: NSLS / Beamline: X25 / 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: 3→45 Å / Num. all: 47514 / Num. obs: 47514 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT1.7data extraction
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→20 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.918 / SU B: 20.136 / SU ML: 0.347 / Cross valid method: THROUGHOUT / ESU R Free: 0.46 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27962 1792 4.9 %RANDOM
Rwork0.23944 ---
obs0.24156 34518 100 %-
all-37461 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 74.315 Å2
Baniso -1Baniso -2Baniso -3
1-9.38 Å20 Å20 Å2
2---1.26 Å20 Å2
3----8.12 Å2
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9989 0 0 37 10026
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02210197
X-RAY DIFFRACTIONr_bond_other_d0.0040.029273
X-RAY DIFFRACTIONr_angle_refined_deg1.7081.96813775
X-RAY DIFFRACTIONr_angle_other_deg1.097321711
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.06151205
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.48624.959484
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.495151940
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.941536
X-RAY DIFFRACTIONr_chiral_restr0.0940.21561
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211035
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022017
X-RAY DIFFRACTIONr_nbd_refined0.2380.32989
X-RAY DIFFRACTIONr_nbd_other0.1730.310364
X-RAY DIFFRACTIONr_nbtor_refined0.2060.55297
X-RAY DIFFRACTIONr_nbtor_other0.1010.56321
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0250.05559
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.38
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2020.336
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0310.054
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8671.57666
X-RAY DIFFRACTIONr_mcbond_other0.1151.52430
X-RAY DIFFRACTIONr_mcangle_it0.99429907
X-RAY DIFFRACTIONr_scbond_it1.23834797
X-RAY DIFFRACTIONr_scangle_it1.9084.53868
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1745tight positional0.060.05
2B1745tight positional0.080.05
3C1745tight positional0.080.05
4D1745tight positional0.070.05
1A2926medium positional0.60.5
2B2926medium positional0.580.5
3C2926medium positional0.570.5
4D2926medium positional0.60.5
1A1745tight thermal0.10.5
2B1745tight thermal0.10.5
3C1745tight thermal0.090.5
4D1745tight thermal0.10.5
1A2926medium thermal0.522
2B2926medium thermal0.52
3C2926medium thermal0.522
4D2926medium thermal0.512
LS refinement shellResolution: 3→3.076 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 50 -
Rwork0.356 2491 -
obs--100 %

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