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- PDB-8s0u: Structure of the LytM domain of PrgK from E. faecalis -

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Basic information

Entry
Database: PDB / ID: 8s0u
TitleStructure of the LytM domain of PrgK from E. faecalis
ComponentsPrgK
KeywordsHYDROLASE / peptidoglycan hydrolases / LytM family / degenerate / regulatory
Function / homologyPhage tail lysozyme / Phage tail lysozyme / CHAP domain profile. / CHAP domain / CHAP domain / Papain-like cysteine peptidase superfamily / membrane / PrgK
Function and homology information
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSun, W.-S. / Berntsson, R.P.-A.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research Council2016-03599 Sweden
Swedish Research Council2023-02423 Sweden
CitationJournal: Mbio / Year: 2024
Title: Breaking barriers: pCF10 type 4 secretion system relies on a self-regulating muramidase to modulate the cell wall.
Authors: Sun, W.-.S. / Torrens, G. / Ter Beek, J. / Cava, F. / Berntsson, R.P.-.A.
History
DepositionFeb 14, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Aug 28, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PrgK
B: PrgK


Theoretical massNumber of molelcules
Total (without water)60,7022
Polymers60,7022
Non-polymers00
Water12,484693
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-1 kcal/mol
Surface area25500 Å2
Unit cell
Length a, b, c (Å)53.320, 53.690, 56.350
Angle α, β, γ (deg.)63.300, 70.370, 70.160
Int Tables number1
Space group name H-MP1
Space group name HallP1

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Components

#1: Protein PrgK


Mass: 30350.924 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: OG1RF pCF10 / Gene: prgK / Plasmid: p7XNH3 / Details (production host): T7 promoter; N-terminal His tag
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q5G3P4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 693 / 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: 2.18 Å3/Da / Density % sol: 43.56 %
Crystal growTemperature: 293.15 K / Method: evaporation / pH: 7.5
Details: 0.2 M Ammonium sulfate, 0.1 M Sodium acetate, pH 4.6, 30 % w/v PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Sep 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→49.13 Å / Num. obs: 76646 / % possible obs: 93.35 % / Redundancy: 1.9 % / Biso Wilson estimate: 16.27 Å2 / CC1/2: 0.911 / CC star: 0.977 / Rmerge(I) obs: 0.08493 / Rrim(I) all: 0.1201 / Net I/σ(I): 6.98
Reflection shellResolution: 1.5→1.554 Å / Rmerge(I) obs: 0.2961 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 7437 / CC1/2: 0.797 / CC star: 0.942 / Rrim(I) all: 0.4187 / % possible all: 90.66

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→49.13 Å / SU ML: 0.156 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 21.0897
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.208 3773 2.61 %
Rwork0.1767 140875 -
obs0.1775 76646 93.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.94 Å2
Refinement stepCycle: LAST / Resolution: 1.5→49.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4236 0 0 693 4929
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01214365
X-RAY DIFFRACTIONf_angle_d1.08965916
X-RAY DIFFRACTIONf_chiral_restr0.0845653
X-RAY DIFFRACTIONf_plane_restr0.0174757
X-RAY DIFFRACTIONf_dihedral_angle_d6.3483566
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.3271600.26675078X-RAY DIFFRACTION85.95
1.52-1.540.2341400.25625120X-RAY DIFFRACTION86.2
1.54-1.560.28141190.24325054X-RAY DIFFRACTION84.94
1.56-1.580.28481390.23634876X-RAY DIFFRACTION83.03
1.58-1.610.29481300.22974887X-RAY DIFFRACTION81.92
1.61-1.630.24871250.21075099X-RAY DIFFRACTION86.43
1.63-1.660.2441400.20265221X-RAY DIFFRACTION87.71
1.66-1.690.20211370.19765089X-RAY DIFFRACTION86.15
1.69-1.720.25051190.18665106X-RAY DIFFRACTION85.8
1.72-1.750.21771560.18645122X-RAY DIFFRACTION86.3
1.75-1.790.24481300.18275161X-RAY DIFFRACTION87.43
1.79-1.820.21641290.18145162X-RAY DIFFRACTION87.43
1.82-1.870.21611600.18775178X-RAY DIFFRACTION87.02
1.87-1.910.23121300.18725112X-RAY DIFFRACTION86.36
1.91-1.970.18111400.16535053X-RAY DIFFRACTION86.12
1.97-2.020.1771250.16234987X-RAY DIFFRACTION84.64
2.02-2.090.1741450.165035X-RAY DIFFRACTION84.04
2.09-2.160.19391260.16364649X-RAY DIFFRACTION79
2.16-2.250.24821210.15774922X-RAY DIFFRACTION82.4
2.25-2.350.23891500.18095213X-RAY DIFFRACTION88.21
2.35-2.480.17451370.17715517X-RAY DIFFRACTION93.89
2.48-2.630.18561550.17985728X-RAY DIFFRACTION96.25
2.63-2.830.24331530.17325794X-RAY DIFFRACTION97.17
2.83-3.120.1881630.18125720X-RAY DIFFRACTION96.92
3.12-3.570.19131410.16345701X-RAY DIFFRACTION96.09
3.57-4.50.2091490.16165578X-RAY DIFFRACTION94.41
4.5-49.130.18541540.17145713X-RAY DIFFRACTION96.5
Refinement TLS params.Method: refined / Origin x: 2.96482453218 Å / Origin y: -13.7921827857 Å / Origin z: -1.98404020609 Å
111213212223313233
T0.0842030549428 Å2-0.0111010903576 Å20.00959879858028 Å2-0.128120427572 Å20.00752790945118 Å2--0.0992155700613 Å2
L0.291516500892 °2-0.13894165229 °2-0.0153061752223 °2-0.858077694436 °20.0124386448887 °2--0.227395811715 °2
S-0.00259639929856 Å °0.00281782289421 Å °0.00166277527665 Å °-0.017657108207 Å °0.00125954810088 Å °-0.022676741135 Å °-0.00640518545527 Å °-0.0283977366551 Å °0.00215656707177 Å °
Refinement TLS groupSelection details: all

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