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- PDB-6z9k: CAP domain of Enterococcal PrgA -

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Basic information

Entry
Database: PDB / ID: 6z9k
TitleCAP domain of Enterococcal PrgA
ComponentsPrgA
KeywordsCELL ADHESION / Protease domain / CAP domain
Function / homologySEC10/PgrA surface exclusion domain / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / extracellular region / metal ion binding / membrane / LPXTG cell wall anchor domain
Function and homology information
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 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 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
B: PrgA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5625
Polymers56,2752
Non-polymers2873
Water11,638646
1
A: PrgA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1622
Polymers28,1381
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PrgA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4003
Polymers28,1381
Non-polymers2632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.874, 35.998, 84.854
Angle α, β, γ (deg.)90.000, 114.470, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PrgA


Mass: 28137.525 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Gene: prgA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q04111
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 646 / Source method: isolated from a natural source / Formula: H2O
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: 2.07 Å3/Da / Density % sol: 40.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.02 M Na/KPO4, 0.1 M Bis-Tris propane pH 6.5, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.078118 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.078118 Å / Relative weight: 1
ReflectionResolution: 1.5→45.7 Å / Num. obs: 72114 / % possible obs: 96.6 % / Redundancy: 4.907 % / Biso Wilson estimate: 27.869 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rrim(I) all: 0.076 / Χ2: 1.011 / Net I/σ(I): 11.55 / Num. measured all: 353880
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
1.5-1.594.3980.9361.26439711191099990.4241.06584
1.59-1.75.0370.662.165633411257111830.6850.73999.3
1.7-1.844.920.3963.575069710481103050.8780.44498.3
1.84-2.015.1010.2016.9649312970696670.970.22599.6
2.01-2.254.9830.10812.0943263877486820.990.12199
2.25-2.65.0860.07317.939154774076980.9950.08199.5
2.6-3.184.9960.05125.3632691661465430.9970.05698.9
3.18-4.484.810.03734.3624579516851100.9980.04198.9
4.48-45.74.7430.03936.8513878296929260.9980.04398.6

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0258refinement
XDSdata reduction
XSCALEdata scaling
SOLVEphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.5→45.7 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / SU B: 3.634 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2013 3653 5.1 %RANDOM
Rwork0.163 ---
obs0.1649 68543 96.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.15 Å2 / Biso mean: 24.022 Å2 / Biso min: 12.56 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å20.06 Å2
2---0.53 Å20 Å2
3---0.61 Å2
Refinement stepCycle: final / Resolution: 1.5→45.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3873 0 17 646 4536
Biso mean--42.76 36.45 -
Num. residues----488
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0134002
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173681
X-RAY DIFFRACTIONr_angle_refined_deg1.761.6435381
X-RAY DIFFRACTIONr_angle_other_deg1.5481.5938657
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9525498
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.16326.021191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.54615786
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.597156
X-RAY DIFFRACTIONr_chiral_restr0.0870.2510
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024430
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02720
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 215 -
Rwork0.32 3755 -
all-3970 -
obs--73.21 %
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)
11.7893-0.6321-0.34160.47550.12030.5644-0.1356-0.09070.090.04880.1188-0.04120.0499-0.03030.01680.017-0.0044-0.00680.0546-0.01030.032792.8525.921457.2357
21.4087-0.13140.0360.43890.11720.7722-0.0243-0.13550.01710.01280.0567-0.0115-0.05480.0354-0.03240.0057-0.0011-0.0010.02830.00720.013951.76177.279557.405
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A300 - 538
2X-RAY DIFFRACTION2B293 - 541

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