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- PDB-5dbl: Crystal structure of the Staphylococcus aureus SasG E1-G52 Y625W ... -

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Basic information

Entry
Database: PDB / ID: 5dbl
TitleCrystal structure of the Staphylococcus aureus SasG E1-G52 Y625W mutant
ComponentsSurface protein G
KeywordsSTRUCTURAL PROTEIN / SasG / Biofilm / Staphylococcus aureus
Function / homology
Function and homology information


single-species submerged biofilm formation / extracellular region
Similarity search - Function
Resuscitation-promoting factor rpfb. / Resuscitation-promoting factor rpfb fold / E domain / E domain / Bacterial lectin / G5 domain / G5 domain / G5 domain profile. / G5 / YSIRK type signal peptide ...Resuscitation-promoting factor rpfb. / Resuscitation-promoting factor rpfb fold / E domain / E domain / Bacterial lectin / G5 domain / G5 domain / G5 domain profile. / G5 / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Single Sheet / Mainly Beta
Similarity search - Domain/homology
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsWhelan, F. / Potts, J.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/J005029/1 United Kingdom
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Disorder drives cooperative folding in a multidomain protein.
Authors: Gruszka, D.T. / Mendonca, C.A. / Paci, E. / Whelan, F. / Hawkhead, J. / Potts, J.R. / Clarke, J.
History
DepositionAug 21, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2016Group: Database references
Revision 1.2Oct 19, 2016Group: Database references
Revision 1.3Nov 9, 2016Group: Database references
Revision 1.4Jan 10, 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: Surface protein G


Theoretical massNumber of molelcules
Total (without water)14,5161
Polymers14,5161
Non-polymers00
Water5,332296
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.046, 34.970, 69.166
Angle α, β, γ (deg.)90.000, 104.890, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-727-

HOH

21A-862-

HOH

31A-913-

HOH

41A-946-

HOH

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Components

#1: Protein Surface protein G


Mass: 14516.241 Da / Num. of mol.: 1 / Fragment: UNP residues 498-629 / Mutation: Y625W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: NCTC 8325 / Gene: sasG, SAOUHSC_02798 / Plasmid: pSKB2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2G2B2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 100 mM citrate pH 5, 20% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.6→33.49 Å / Num. obs: 21092 / % possible obs: 99 % / Redundancy: 3.2 % / Biso Wilson estimate: 17.47 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.04 / Net I/σ(I): 11.1 / Num. measured all: 67910 / Scaling rejects: 3
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.2 % / Rejects: _

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.6-1.630.731.6319510040.7710.48498.5
8.76-33.490.02634.842513310.01790.8

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Processing

Software
NameVersionClassification
PHENIXdev_1839refinement
XDSNovember 3, 2014data reduction
XDSNovember 3, 2014data scaling
Aimless0.5.12data scaling
PHASER2.5.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TIP

3tip


Resolution: 1.6→33.422 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2072 1074 5.1 %RANDOM
Rwork0.1739 19974 --
obs0.1757 21048 98.62 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.65 Å2 / Biso mean: 24.5601 Å2 / Biso min: 12.15 Å2
Refinement stepCycle: final / Resolution: 1.6→33.422 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1005 0 0 298 1303
Biso mean---34.07 -
Num. residues----130
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061090
X-RAY DIFFRACTIONf_angle_d0.9921488
X-RAY DIFFRACTIONf_chiral_restr0.04161
X-RAY DIFFRACTIONf_plane_restr0.005204
X-RAY DIFFRACTIONf_dihedral_angle_d13.644455
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.67290.31271380.28542455259398
1.6729-1.76110.26821580.24542453261199
1.7611-1.87140.20771180.20132463258198
1.8714-2.01590.24071350.19022486262198
2.0159-2.21870.20351180.16312515263399
2.2187-2.53960.18891300.1772500263099
2.5396-3.19930.20611240.17282547267199
3.1993-33.42890.1881530.14682555270898
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)
10.0398-0.0059-0.00280.07780.02240.0053-0.07620.12640.0614-0.08530.0040.0080.11960.006900.169-0.02360.01010.21240.02090.195436.6068-25.349561.625
20.01760.03340.00680.0164-0.07120.01190.1142-0.0007-0.0391-0.1031-0.05840.09270.1933-0.013800.22120.0173-0.01240.1776-0.00710.194741.042-33.044669.4406
30.01660.00780.00320.0097-0.0004-0.00030.08410.1311-0.091-0.2158-0.0166-0.00050.034-0.068900.1968-0.0007-0.00740.18550.0070.180124.0561-22.480146.3018
4-0.0125-0.03590.0381-0.02540.04060.0065-0.03480.01220.0622-0.0601-0.0146-0.04440.0003-0.013100.1752-0.0062-0.00860.167-0.00170.186935.7671-27.520263.5708
5-0.1188-0.0110.0586-0.05460.00450.0164-0.0289-0.027-0.02710.0610.0708-0.0619-0.30480.230100.1904-0.0290.0030.231-0.00120.157949.5764-26.841797.5138
60.02410.03130.17370.06560.20890.77530.02710.01160.0499-0.1097-0.0195-0.01790.27-0.2024-0.00360.1141-0.00550.00340.2240.010.183855.9241-31.7719129.2222
70.00550.0115-0.01530.0206-0.00270.0070.0759-0.0686-0.11010.02510.0720.04330.2808-0.0326-00.14850.01390.01210.16020.0010.183866.692-33.6196141.96
80.08660.0081-0.0189-0.0002-0.0001-0.0041-0.05710.10650.1142-0.0117-0.020.0146-0.0968-0.2001-00.14250.00160.00770.19540.01190.163661.3763-26.7325126.8654
9-0.13680.01310.3004-0.14170.01370.11520.06910.0196-0.0465-0.01110.0249-0.00010.10560.16690.00030.19780.0204-0.00870.21940.00380.1551.2553-29.9967106.9236
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 500 through 510 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 511 through 527 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 528 through 537 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 538 through 547 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 548 through 561 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 562 through 569 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 570 through 577 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 578 through 586 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 587 through 629 )A0

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