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- PDB-4wve: Crystal structure of the Staphylococcus aureus SasG G52-E2-G53 module -

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Basic information

Entry
Database: PDB / ID: 4wve
TitleCrystal structure of the Staphylococcus aureus SasG G52-E2-G53 module
ComponentsSurface protein G
KeywordsSTRUCTURAL PROTEIN / single-layer beta sheet / biofilm formation / surface
Function / homology
Function and homology information


single-species submerged biofilm formation / extracellular region
Similarity search - Function
Resuscitation-promoting factor rpfb fold - #30 / 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 fold - #30 / 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 / 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: Nat Commun / Year: 2015
Title: Cooperative folding of intrinsically disordered domains drives assembly of a strong elongated protein.
Authors: Gruszka, D.T. / Whelan, F. / Farrance, O.E. / Fung, H.K. / Paci, E. / Jeffries, C.M. / Svergun, D.I. / Baldock, C. / Baumann, C.G. / Brockwell, D.J. / Potts, J.R. / Clarke, J.
History
DepositionNov 5, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2015Group: Database references
Revision 1.2Jun 17, 2015Group: Database references
Revision 2.0Aug 30, 2017Group: Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / pdbx_audit_support / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.occupancy / _pdbx_audit_support.funding_organization / _struct_site_gen.auth_seq_id
Revision 2.1Jan 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Surface protein G
B: Surface protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4193
Polymers47,3832
Non-polymers351
Water4,630257
1
A: Surface protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7272
Polymers23,6921
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Surface protein G


Theoretical massNumber of molelcules
Total (without water)23,6921
Polymers23,6921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.861, 45.628, 60.359
Angle α, β, γ (deg.)84.760, 83.220, 78.600
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 0 / Auth seq-ID: 552 - 756 / Label seq-ID: 10 - 214

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Surface protein G /


Mass: 23691.529 Da / Num. of mol.: 2 / Fragment: UNP residues 545-757
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 (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2G2B2
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 2.25 Å3/Da / Density % sol: 45.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M magnesium chloride, 0.1 M HEPES, 30% PEG400, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.6→59.79 Å / Num. obs: 53868 / % possible obs: 98.9 % / Redundancy: 4.3 % / Biso Wilson estimate: 14.4 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.05 / Net I/σ(I): 15.8 / Num. measured all: 225293 / Scaling rejects: 717
Reflection shell

Diffraction-ID: 1 / Redundancy: 4.3 % / Rejects: 0

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.6-1.630.5114.61126026310.9290.27897.9
8.76-59.790.0783914173280.990.04198.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDS0.2.17data reduction
Aimless0.2.17data scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TIP
Resolution: 1.6→59.79 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.2664 / WRfactor Rwork: 0.2244 / FOM work R set: 0.8058 / SU B: 4.482 / SU ML: 0.081 / SU R Cruickshank DPI: 0.1043 / SU Rfree: 0.1068 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.249 2694 5 %RANDOM
Rwork0.2071 50959 --
obs0.2093 50959 98.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 56.9 Å2 / Biso mean: 25.569 Å2 / Biso min: 11.53 Å2
Baniso -1Baniso -2Baniso -3
1-1.79 Å20.42 Å20.05 Å2
2---0.28 Å21.2 Å2
3----1.14 Å2
Refinement stepCycle: final / Resolution: 1.6→59.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3170 0 1 257 3428
Biso mean--16.5 31.49 -
Num. residues----420
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.023321
X-RAY DIFFRACTIONr_bond_other_d0.0050.023155
X-RAY DIFFRACTIONr_angle_refined_deg1.7252.0184531
X-RAY DIFFRACTIONr_angle_other_deg1.11537426
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0535440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.10226.803122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.53915596
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9021510
X-RAY DIFFRACTIONr_chiral_restr0.1010.2518
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0223692
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02546
X-RAY DIFFRACTIONr_mcbond_it1.3461.461718
X-RAY DIFFRACTIONr_mcbond_other1.3471.461717
X-RAY DIFFRACTIONr_mcangle_it2.0072.1892157
Refine LS restraints NCS

Ens-ID: 1 / Number: 10074 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.14 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.6420.2921850.2673686X-RAY DIFFRACTION96.27
1.642-1.6870.282250.2473575X-RAY DIFFRACTION96.643
1.687-1.7350.2861910.2343541X-RAY DIFFRACTION97.441
1.735-1.7890.291490.2263432X-RAY DIFFRACTION97.735
1.789-1.8470.2661640.2193372X-RAY DIFFRACTION97.68
1.847-1.9120.2411700.2163257X-RAY DIFFRACTION98.449
1.912-1.9840.2091580.2043158X-RAY DIFFRACTION98.31
1.984-2.0650.2691640.2182994X-RAY DIFFRACTION98.227
2.065-2.1570.2451610.2122915X-RAY DIFFRACTION98.97
2.157-2.2620.2541420.2092787X-RAY DIFFRACTION99.087
2.262-2.3840.2731410.2072664X-RAY DIFFRACTION99.398
2.384-2.5290.2361360.2082527X-RAY DIFFRACTION99.514
2.529-2.7030.2371180.2192356X-RAY DIFFRACTION99.678
2.703-2.9190.2741100.2282197X-RAY DIFFRACTION99.697
2.919-3.1970.2061120.2022033X-RAY DIFFRACTION99.721
3.197-3.5730.288990.2071842X-RAY DIFFRACTION99.949
3.573-4.1230.2631000.1871610X-RAY DIFFRACTION99.942
4.123-5.0440.195800.1651374X-RAY DIFFRACTION100
5.044-7.1070.243540.2061051X-RAY DIFFRACTION99.91
7.107-59.790.278350.21587X-RAY DIFFRACTION99.52
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.1744-0.52710.90331.9459-3.37155.8772-0.0012-0.0205-0.00640.10270.0262-0.0076-0.1784-0.0184-0.0250.1067-0.0057-0.02970.0493-0.01330.0607-4.2119-31.446148.512
20.0348-0.12150.27480.6245-1.42343.43460.049-0.0061-0.0138-0.07370.04820.04330.15490.0148-0.09720.113-0.0013-0.01590.0849-0.00120.038-6.5262-24.239824.9883
30.1340.2826-0.40981.5751-2.55764.19250.04850.00380.02850.106-0.05680.0176-0.13870.10910.00830.11710.03840.02510.05580.00680.0567-1.45227.3762-50.828
40.0548-0.32370.31352.0142-1.95911.9086-0.0037-0.0099-0.0107-0.076-0.00370.0070.07130.00910.00740.140.05960.01370.03990.03730.0705-27.5454-4.7672-2.3397
50.22310.4654-0.41376.3925-6.61746.888-0.0193-0.0327-0.028-0.2789-0.0634-0.05860.2820.05720.08260.07090.03690.02540.07260.01210.1049-24.1865-45.614932.4773
60.27250.6627-0.74812.8057-3.3714.39320.17160.03230.07710.00390.0340.30580.09320.2094-0.20570.21790.05970.02180.16120.1050.1003-27.6122-73.830662.7542
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A543 - 588
2X-RAY DIFFRACTION2A589 - 677
3X-RAY DIFFRACTION3A678 - 757
4X-RAY DIFFRACTION4B551 - 651
5X-RAY DIFFRACTION5B652 - 694
6X-RAY DIFFRACTION6B695 - 757

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