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- PDB-2aw6: Structure of a bacterial peptide pheromone/receptor complex and i... -

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Basic information

Entry
Database: PDB / ID: 2aw6
TitleStructure of a bacterial peptide pheromone/receptor complex and its mechanism of gene regulation
Components
  • PrgX
  • peptide
KeywordsTRANSCRIPTION / Repressor / pheromone / DNA binding / regulatory
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 ...: / 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
DepositionAug 31, 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.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 23, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: PrgX
B: PrgX
E: peptide
F: peptide


Theoretical massNumber of molelcules
Total (without water)75,8554
Polymers75,8554
Non-polymers00
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8490 Å2
ΔGint-46 kcal/mol
Surface area25650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.546, 82.546, 380.156
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 2 / Auth seq-ID: 1 - 286 / Label seq-ID: 1 - 286

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein PrgX


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


Mass: 790.001 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 53.2 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7
Details: PEG4000, citrate-phosphate, pH 7.0, EVAPORATION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2
DetectorDate: Mar 2, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3→47.42 Å / Num. obs: 16419 / % possible obs: 94.9 % / Observed criterion σ(F): 1.2 / Observed criterion σ(I): 1.5 / Redundancy: 5.97 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 10
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 2.1 / % possible all: 94.9

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
CNSrefinement
PDB_EXTRACT1.7data extraction
d*TREKdata scaling
d*TREK9.2LDzdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2AWI

2awi


Resolution: 3→30 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.895 / SU B: 18.294 / SU ML: 0.32 / Cross valid method: THROUGHOUT / ESU R: 3.058 / ESU R Free: 0.462 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25987 784 5 %RANDOM
Rwork0.21194 ---
obs0.21435 14829 95.27 %-
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: 54.506 Å2
Baniso -1Baniso -2Baniso -3
1-1.33 Å20.67 Å20 Å2
2--1.33 Å20 Å2
3----2 Å2
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4841 0 0 25 4866
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224935
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.081.9696664
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4045583
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.4624.892231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.23215944
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4121518
X-RAY DIFFRACTIONr_chiral_restr0.0780.2767
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023618
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.220.22592
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.23565
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.2179
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.221
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1144tight positional0.030.05
1216medium positional0.310.5
LS refinement shellResolution: 3→3.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 36 -
Rwork0.314 764 -
obs--68.49 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param

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