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- PDB-6z9l: Enterococcal PrgA -

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Basic information

Entry
Database: PDB / ID: 6z9l
TitleEnterococcal PrgA
Components
  • Poly-alanine peptide
  • PrgA
KeywordsCELL ADHESION / Protease domain / CAP domain / coiled-coil
Function / homologySEC10/PgrA surface exclusion domain / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / membrane / PrgA
Function and homology information
Biological speciesEnterococcus faecalis (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.063 Å
AuthorsBerntsson, R.P.A. / Schmitt, A.
Funding support Sweden, 3items
OrganizationGrant numberCountry
Swedish Research Council2016-03599 Sweden
Other privateJCK-1524 Sweden
Other privateSMK-1869 Sweden
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Enterococcal PrgA Extends Far Outside the Cell and Provides Surface Exclusion to Protect against Unwanted Conjugation.
Authors: Schmitt, A. / Hirt, H. / Jarva, M.A. / Sun, W.S. / Ter Beek, J. / Dunny, G.M. / Berntsson, R.P.
History
DepositionJun 4, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 24, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PrgA
F: Poly-alanine peptide
G: Poly-alanine peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,91017
Polymers88,5663
Non-polymers1,34514
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-137 kcal/mol
Surface area49570 Å2
Unit cell
Length a, b, c (Å)126.356, 126.356, 293.908
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein PrgA


Mass: 87250.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Gene: prgA / Production host: Escherichia coli (E. coli) / References: UniProt: Q04111
#2: Protein/peptide Poly-alanine peptide


Mass: 657.715 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
Has ligand of interestN

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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: 6.62 Å3/Da / Density % sol: 83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 37.5% (v/v) PEG400, 0.1 M Tris/HCl (pH 8.5), 0.114 M LiSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976247 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976247 Å / Relative weight: 1
ReflectionResolution: 3.06→49.107 Å / Num. obs: 45500 / % possible obs: 99.5 % / Redundancy: 12.682 % / Biso Wilson estimate: 102.72 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.255 / Rrim(I) all: 0.266 / Χ2: 1.076 / Net I/σ(I): 8.56 / Num. measured all: 577045
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.06-3.2511.2212.5880.7579085724970480.3422.7197.2
3.25-3.4713.731.741.4593131678467830.5891.807100
3.47-3.7512.8730.912.9581884636163610.8520.949100
3.75-4.113.1050.4526.477322590059000.9680.471100
4.1-4.5812.7620.26810.368239534853470.9860.279100
4.58-5.2812.9580.1813.261760476747660.9950.188100
5.28-6.4512.5920.20912.0451440408540850.9890.218100
6.45-9.0512.6630.09824.6941105324732460.9980.102100
9.05-49.10711.7510.06235.8523079198619640.9980.06598.9

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Processing

Software
NameVersionClassification
PHENIX1.10.1refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Z9K

6z9k


Resolution: 3.063→49.107 Å / SU ML: 0.56 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 36.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3182 2099 4.62 %
Rwork0.2865 43374 -
obs0.2879 45473 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 598.68 Å2 / Biso mean: 134.9054 Å2 / Biso min: 32.99 Å2
Refinement stepCycle: final / Resolution: 3.063→49.107 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5878 0 70 0 5948
Biso mean--166.7 --
Num. residues----762
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035972
X-RAY DIFFRACTIONf_angle_d0.5768044
X-RAY DIFFRACTIONf_chiral_restr0.033920
X-RAY DIFFRACTIONf_plane_restr0.0021064
X-RAY DIFFRACTIONf_dihedral_angle_d16.7933771
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.063-3.13410.40011280.4291265693
3.1341-3.21250.42741380.41622851100
3.2125-3.29930.36921380.39562839100
3.2993-3.39640.33751380.37192869100
3.3964-3.5060.39411390.37152874100
3.506-3.63120.38861380.34852847100
3.6312-3.77660.31741390.31752871100
3.7766-3.94840.31551400.2772886100
3.9484-4.15640.27451380.25622881100
4.1564-4.41670.28981400.24782883100
4.4167-4.75750.30491400.25952902100
4.7575-5.23570.3091420.26432930100
5.2357-5.99220.39891430.31642944100
5.9922-7.54510.31961440.29142984100
7.5451-49.1070.27561540.24163157100

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