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- PDB-6ged: Adhesin domain of PrgB from Enterococcus faecalis bound to DNA -

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Basic information

Entry
Database: PDB / ID: 6ged
TitleAdhesin domain of PrgB from Enterococcus faecalis bound to DNA
Components
  • DNA (5'-D(P*CP*GP*GP*GP*CP*CP*GP*CP*CP*C)-3')
  • DNA (5'-D(P*GP*GP*GP*CP*GP*GP*CP*CP*CP*G)-3')
  • PrgB
KeywordsCELL ADHESION / Adhesin / Biofilm formation
Function / homology
Function and homology information


extracellular region / membrane
Similarity search - Function
Glucan-binding protein C/Surface antigen I/II, V-domain / Glucan-binding protein C/Surface antigen I/II, V-domain superfamily / Glucan-binding protein C / Adhesin isopeptide-forming adherence domain / Cell surface antigen, C-terminal / Antigen I/II, N-terminal / Cell surface antigen C-terminus / Cell surface antigen I/II C2 terminal domain / Adhesin P1 N-terminal domain / KxYKxGKxW signal peptide ...Glucan-binding protein C/Surface antigen I/II, V-domain / Glucan-binding protein C/Surface antigen I/II, V-domain superfamily / Glucan-binding protein C / Adhesin isopeptide-forming adherence domain / Cell surface antigen, C-terminal / Antigen I/II, N-terminal / Cell surface antigen C-terminus / Cell surface antigen I/II C2 terminal domain / Adhesin P1 N-terminal domain / KxYKxGKxW signal peptide / KxYKxGKxW signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain
Similarity search - Domain/homology
Biological speciesEnterococcus faecalis (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.794 Å
AuthorsSchmitt, A. / Berntsson, R.P.A.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research Council2016-03599 Sweden
KempestiftelsernaJCK-1524 Sweden
CitationJournal: Mol. Microbiol. / Year: 2018
Title: PrgB promotes aggregation, biofilm formation, and conjugation through DNA binding and compaction.
Authors: Schmitt, A. / Jiang, K. / Camacho, M.I. / Jonna, V.R. / Hofer, A. / Westerlund, F. / Christie, P.J. / Berntsson, R.P.
History
DepositionApr 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Aug 14, 2019Group: Data collection / Category: reflns / Item: _reflns.pdbx_Rrim_I_all
Revision 1.3Jan 17, 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: PrgB
C: DNA (5'-D(P*GP*GP*GP*CP*GP*GP*CP*CP*CP*G)-3')
D: DNA (5'-D(P*CP*GP*GP*GP*CP*CP*GP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3405
Polymers40,2553
Non-polymers852
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-24 kcal/mol
Surface area15520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.017, 93.026, 99.097
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein PrgB


Mass: 34161.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Gene: prgB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q04112

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DNA chain , 2 types, 2 molecules CD

#2: DNA chain DNA (5'-D(P*GP*GP*GP*CP*GP*GP*CP*CP*CP*G)-3')


Mass: 3087.004 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*CP*GP*GP*GP*CP*CP*GP*CP*CP*C)-3')


Mass: 3006.957 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 164 molecules

#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 1.95 Å3/Da / Density % sol: 36.87 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.12 M Ethylene Glycol, 0.1 M Bicine/Tris pH 8.5, 20% (v/v) Glycerol, 10% (w/v) Polythyleneglycol 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.79→43.732 Å / Num. obs: 28379 / % possible obs: 99.3 % / Redundancy: 13.36 % / CC1/2: 0.999 / Rrim(I) all: 0.172 / Net I/σ(I): 14.22
Reflection shellResolution: 1.79→1.9 Å / Mean I/σ(I) obs: 1.63 / CC1/2: 0.71 / Rrim(I) all: 1.67 / % possible all: 98.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.12_2829refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EVT

6evt
PDB Unreleased entry


Resolution: 1.794→43.732 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.93
RfactorNum. reflection% reflection
Rfree0.212 1419 5 %
Rwork0.1743 --
obs0.1762 28358 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 110.18 Å2 / Biso mean: 33.9533 Å2 / Biso min: 15.43 Å2
Refinement stepCycle: final / Resolution: 1.794→43.732 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2244 410 5 162 2821
Biso mean--44.47 38.35 -
Num. residues----315
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122753
X-RAY DIFFRACTIONf_angle_d1.1523792
X-RAY DIFFRACTIONf_chiral_restr0.072414
X-RAY DIFFRACTIONf_plane_restr0.008423
X-RAY DIFFRACTIONf_dihedral_angle_d12.6451545
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7943-1.85840.35111370.3292594273198
1.8584-1.93290.26461380.25282633277199
1.9329-2.02080.26951410.205526702811100
2.0208-2.12740.25191410.192426732814100
2.1274-2.26060.20981410.172726862827100
2.2606-2.43520.21081410.159926812822100
2.4352-2.68020.18741440.15427312875100
2.6802-3.0680.16241420.147226992841100
3.068-3.86490.19431410.14672669281096
3.8649-43.7450.21451530.178329033056100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.7738-0.1370.13742.37740.19321.27290.0336-0.0956-0.09030.1644-0.04590.0020.0601-0.0252-0.00290.2205-0.0103-0.03480.20980.00590.207640.503923.30627.1535
21.15680.14260.8480.3821-0.05911.38790.05330.07090.0393-0.0798-0.0689-0.0758-0.0155-0.003700.17650.0070.00560.20710.00870.187135.220923.635410.926
30.2435-0.1422-0.27180.48330.65640.9219-0.6228-0.18490.11180.27910.0130.24460.0063-0.1294-0.80790.6356-0.1058-0.13560.35420.20660.54839.59698.081347.327
40.10750.05140.00090.22950.17350.14450.3211-0.04920.04250.30960.13530.21780.4219-0.11620.05961.57460.08510.20351.0838-0.03080.840839.10738.419748.4979
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 260 through 435 )A260 - 435
2X-RAY DIFFRACTION2chain 'A' and (resid 436 through 554 )A436 - 554
3X-RAY DIFFRACTION3chain 'C' and (resid 1 through 10 )C1 - 10
4X-RAY DIFFRACTION4chain 'D' and (resid 1 through 10 )D1 - 10

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