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- PDB-6evu: Adhesin domain of PrgB from Enterococcus faecalis -

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Basic information

Entry
Database: PDB / ID: 6evu
TitleAdhesin domain of PrgB from Enterococcus faecalis
ComponentsPrgB
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
PHOSPHATE ION / PrgB
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.598 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
DepositionNov 2, 2017Deposition 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PrgB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3783
Polymers34,1611
Non-polymers2172
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint-2 kcal/mol
Surface area13990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.550, 60.550, 153.320
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-717-

HOH

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Components

#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
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.07 Å3/Da / Density % sol: 40.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Bicine/Tris pH 8.5 0.12 M Ethylene Glycol 20% (v/v) Glycerol 10% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.975637 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975637 Å / Relative weight: 1
ReflectionResolution: 1.59→47.52 Å / Num. obs: 38693 / % possible obs: 99.9 % / Redundancy: 18.83 % / Net I/σ(I): 28.98
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 16.2 % / Num. unique all: 6091 / CC1/2: 0.643 / Rrim(I) all: 1.627 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.598→47.516 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.99
RfactorNum. reflection% reflection
Rfree0.2269 1935 5 %
Rwork0.19 --
obs0.1919 38685 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 120.95 Å2 / Biso mean: 44.7016 Å2 / Biso min: 18.03 Å2
Refinement stepCycle: final / Resolution: 1.598→47.516 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2397 0 13 199 2609
Biso mean--35.12 44.9 -
Num. residues----313
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142468
X-RAY DIFFRACTIONf_angle_d1.3033329
X-RAY DIFFRACTIONf_chiral_restr0.08355
X-RAY DIFFRACTIONf_plane_restr0.009434
X-RAY DIFFRACTIONf_dihedral_angle_d3.1942012
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5982-1.63820.36691340.32322547268199
1.6382-1.68250.32871360.283625842720100
1.6825-1.7320.32231360.26925782714100
1.732-1.78790.31211350.260425622697100
1.7879-1.85180.27781360.248225842720100
1.8518-1.92590.29541350.240725722707100
1.9259-2.01360.26761380.225126212759100
2.0136-2.11970.27141360.213525852721100
2.1197-2.25250.25971390.212726422781100
2.2525-2.42650.26991380.212526172755100
2.4265-2.67060.28761380.207226342772100
2.6706-3.0570.23781400.199226622802100
3.057-3.85120.20311420.168526982840100
3.8512-47.53690.17021520.153428643016100
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)
10.16130.0918-0.15910.0458-0.1230.25480.4036-0.9739-0.79760.8750.23560.72370.117-0.56620.10990.95760.10390.01411.24760.25750.9602-19.916146.7647-15.988
21.16160.6375-0.0242.4159-1.16780.6429-0.33980.5916-0.3754-0.99670.0991-0.60320.45640.0347-0.3030.42240.03440.12150.3333-0.04180.36766.067826.7918-15.07
33.54151.7197-1.42553.0709-0.67362.1364-0.09210.0622-0.3054-0.2471-0.0202-0.1971-0.0015-0.02860.00650.23970.02940.03650.1963-0.04020.2234-3.051922.6514-3.2624
40.20890.2197-0.33971.5561-0.04080.95040.11280.5370.3403-0.54610.15420.4249-0.3492-0.46510.23420.42340.0662-0.06680.44430.09130.3341-13.284132.069-13.2203
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 246 through 265 )A246 - 265
2X-RAY DIFFRACTION2chain 'A' and (resid 266 through 290 )A266 - 290
3X-RAY DIFFRACTION3chain 'A' and (resid 291 through 453 )A291 - 453
4X-RAY DIFFRACTION4chain 'A' and (resid 454 through 558 )A454 - 558

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