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- PDB-7smh: Structure of SASG A-domain (residues 163-419) from Staphylococcus... -

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Basic information

Entry
Database: PDB / ID: 7smh
TitleStructure of SASG A-domain (residues 163-419) from Staphylococcus aureus
ComponentsSurface protein G
KeywordsCELL ADHESION / L-type lectin
Function / homology
Function and homology information


single-species submerged biofilm formation / extracellular region
Similarity search - Function
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 ...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
Similarity search - Domain/homology
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsAtkin, K.E. / Whelan, F. / Brentnall, A.S. / Dodson, E.J. / Turkenburg, J.P. / Potts, J.R.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/J005029/ United Kingdom
British Heart FoundationFS/12/36/29588 United Kingdom
British Heart FoundationPG/17/19/32862 United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Staphylococcal Periscope proteins Aap, SasG, and Pls project noncanonical legume-like lectin adhesin domains from the bacterial surface.
Authors: Clark, L.C. / Atkin, K.E. / Whelan, F. / Brentnall, A.S. / Harris, G. / Towell, A.M. / Turkenburg, J.P. / Liu, Y. / Feizi, T. / Griffiths, S.C. / Geoghegan, J.A. / Potts, J.R.
History
DepositionOct 25, 2021Deposition site: RCSB / Processing site: RCSB
SupersessionNov 2, 2022ID: 4CD9
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1May 3, 2023Group: Database references / Refinement description / Category: citation / citation_author / struct_ncs_dom_lim
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)123,10911
Polymers122,7634
Non-polymers3477
Water6,251347
1
A: Surface protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7933
Polymers30,6911
Non-polymers1022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Surface protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7312
Polymers30,6911
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Surface protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8554
Polymers30,6911
Non-polymers1643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Surface protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7312
Polymers30,6911
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.210, 63.210, 273.360
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: THR / Beg label comp-ID: THR / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAAA164 - 41921 - 276
21ALAALABB164 - 41921 - 276
12GLUGLUAA164 - 41821 - 275
22GLUGLUCC164 - 41821 - 275
13ALAALAAA164 - 41921 - 276
23ALAALADD164 - 41921 - 276
14ALAALABB164 - 41921 - 276
24ALAALACC164 - 41921 - 276
15ALAALABB164 - 41921 - 276
25ALAALADD164 - 41921 - 276
16ALAALACC164 - 41921 - 276
26ALAALADD164 - 41921 - 276

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Surface protein G


Mass: 30690.693 Da / Num. of mol.: 4 / Fragment: A domain (UNP residues 144-423)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain NCTC 8325 / PS 47) (bacteria)
Strain: NCTC 8325 / PS 47 / Gene: sasG, SAOUHSC_02798 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2G2B2
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.41 Å3/Da / Density % sol: 49.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 20% PEG3350, 0.2 M sodium malonate, pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2013 / Details: MIRRORS
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.506
11K, H, -L20.494
ReflectionResolution: 1.65→68.34 Å / Num. obs: 127888 / % possible obs: 99.8 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 14
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 6174 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 7SIE

7sie


Resolution: 1.65→57.37 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.928 / SU B: 1.637 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.02 / ESU R Free: 0.021 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.226 6410 5.1 %RANDOM
Rwork0.1855 ---
obs0.1875 120320 99.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 60.13 Å2 / Biso mean: 16.33 Å2 / Biso min: 2.62 Å2
Baniso -1Baniso -2Baniso -3
1--0.64 Å2-0 Å2-0 Å2
2---0.64 Å2-0 Å2
3---1.28 Å2
Refinement stepCycle: final / Resolution: 1.65→57.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7878 0 16 354 8248
Biso mean--21.57 16.69 -
Num. residues----1022
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0138111
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167382
X-RAY DIFFRACTIONr_angle_refined_deg1.9171.64110885
X-RAY DIFFRACTIONr_angle_other_deg1.431.59316988
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.46851028
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.57224.486428
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.921151365
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5011528
X-RAY DIFFRACTIONr_chiral_restr0.0950.21038
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.029550
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021994
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A78000.14
12B78000.14
21A77730.15
22C77730.15
31A77780.15
32D77780.15
41B78450.14
42C78450.14
51B76380.16
52D76380.16
61C77180.15
62D77180.15
LS refinement shellResolution: 1.65→1.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 480 -
Rwork0.228 8642 -
all-9122 -
obs--96.58 %

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