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- PDB-4faj: Structure and mode of peptide binding of pheromone receptor PrgZ -

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Basic information

Entry
Database: PDB / ID: 4faj
TitleStructure and mode of peptide binding of pheromone receptor PrgZ
Components
  • PrgZ
  • Sex pheromone cCF10
KeywordsPEPTIDE BINDING PROTEIN / Substrate Binding Protein / pheromone / Extracellular / membrane anchored
Function / homology
Function and homology information


pheromone activity / peptide transmembrane transporter activity / peptide transport / ATP-binding cassette (ABC) transporter complex / outer membrane-bounded periplasmic space / metal ion binding
Similarity search - Function
Dipeptide-binding Protein; domain 1 / Dipeptide-binding Protein; Domain 1 / Solute-binding protein family 5, conserved site / Bacterial extracellular solute-binding proteins, family 5 signature. / Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle ...Dipeptide-binding Protein; domain 1 / Dipeptide-binding Protein; Domain 1 / Solute-binding protein family 5, conserved site / Bacterial extracellular solute-binding proteins, family 5 signature. / Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Roll / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Sex pheromone cCF10 / PrgZ
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsBerntsson, R.P.-A. / Schuurman-Wolters, G.K. / Dunny, K. / Slotboom, D.J. / Poolman, B.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structure and Mode of Peptide Binding of Pheromone Receptor PrgZ.
Authors: Berntsson, R.P. / Schuurman-Wolters, G.K. / Dunny, G. / Slotboom, D.J. / Poolman, B.
History
DepositionMay 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references / Derived calculations
Revision 1.2Dec 12, 2012Group: Derived calculations
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PrgZ
B: Sex pheromone cCF10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,56410
Polymers63,9342
Non-polymers6308
Water7,566420
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-16 kcal/mol
Surface area21220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.622, 74.122, 112.622
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PrgZ


Mass: 63143.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Gene: prgZ / Production host: Escherichia coli (E. coli) / References: UniProt: Q51643
#2: Protein/peptide Sex pheromone cCF10


Mass: 790.001 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthesized cCF10 peptide / Source: (synth.) Enterococcus faecalis (bacteria) / References: UniProt: P20104
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 420 / 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: 2.24 Å3/Da / Density % sol: 45.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.01 M Zinc sulfate, 0.1 M MES, 25% w/v PEG 550 MME, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 28, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.9→45.97 Å / Num. obs: 45969 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 28.977 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 13.79
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.9-2.010.7162.2835000721198.2
2.01-2.150.4233.9134104690299.9
2.15-2.320.2755.92318516459100
2.32-2.540.1958.2829506596799.9
2.54-2.840.12612.326626540099.9
2.84-3.280.07419.423523480499.9
3.28-4.010.04131.9119886410399.8
4.01-5.660.03140.615407323299.9
5.660.02742.788514189199.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 58.86 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å45.97 Å
Translation2.5 Å45.97 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / Highest resolution: 1.9 Å / WRfactor Rfree: 0.1854 / WRfactor Rwork: 0.1497 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.9171 / SU B: 4.899 / SU ML: 0.07 / SU R Cruickshank DPI: 0.1278 / SU Rfree: 0.1205 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1928 2297 5 %RANDOM
Rwork0.1557 ---
obs0.1575 45929 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 93.3 Å2 / Biso mean: 23.2727 Å2 / Biso min: 10.4 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Highest resolution: 1.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4038 0 28 420 4486
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224220
X-RAY DIFFRACTIONr_bond_other_d0.0010.022846
X-RAY DIFFRACTIONr_angle_refined_deg1.1151.975712
X-RAY DIFFRACTIONr_angle_other_deg0.82937051
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5495533
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.79426.72186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.3515789
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.91158
X-RAY DIFFRACTIONr_chiral_restr0.0690.2644
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024674
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02747
X-RAY DIFFRACTIONr_mcbond_it0.5591.52622
X-RAY DIFFRACTIONr_mcbond_other0.1231.51059
X-RAY DIFFRACTIONr_mcangle_it1.05724252
X-RAY DIFFRACTIONr_scbond_it1.70931598
X-RAY DIFFRACTIONr_scangle_it2.9034.51460
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.198 166 -
Rwork0.164 3156 -
all-3322 -
obs--99.46 %
Refinement TLS params.Method: refined / Origin x: 33.9728 Å / Origin y: 4.3213 Å / Origin z: 11.5281 Å
111213212223313233
T0.0188 Å2-0.0158 Å2-0.0036 Å2-0.0149 Å2-0.0011 Å2--0.0338 Å2
L0.4824 °2-0.1277 °2-0.1805 °2-0.3818 °2-0.0779 °2--0.558 °2
S-0.0173 Å °0.0228 Å °-0.0442 Å °0.0121 Å °0.0006 Å °0.0107 Å °0.0377 Å °-0.0255 Å °0.0167 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A58 - 564
2X-RAY DIFFRACTION1A601 - 608
3X-RAY DIFFRACTION1A701 - 1111

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