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- PDB-7avk: Streptococcal High Identity Repeats in Tandem (SHIRT) domain 10 f... -

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Basic information

Entry
Database: PDB / ID: 7avk
TitleStreptococcal High Identity Repeats in Tandem (SHIRT) domain 10 from cell surface protein SGO_0707
ComponentsLPXTG cell wall surface protein
KeywordsCELL ADHESION / Bacterial surface / adhesin / tandem repeat / Sgo0707
Function / homology
Function and homology information


SHIRT domain / Sgo0707, N-terminal domain / SHIRT domain / Sgo0707 N-terminal domain / Sgo0707-like, N2 domain / Sgo0707 N2 domain / Fimbrial isopeptide formation D2 domain / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain
Similarity search - Domain/homology
isothiocyanate / LPXTG cell wall surface protein
Similarity search - Component
Biological speciesStreptococcus gordonii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.82 Å
AuthorsDegut, C. / Gilburt, J. / Whelan, F. / Jenkins, H.T. / Potts, J.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/J005029/1 United Kingdom
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Periscope Proteins are variable-length regulators of bacterial cell surface interactions.
Authors: Whelan, F. / Lafita, A. / Gilburt, J. / Degut, C. / Griffiths, S.C. / Jenkins, H.T. / St John, A.N. / Paci, E. / Moir, J.W.B. / Plevin, M.J. / Baumann, C.G. / Bateman, A. / Potts, J.R.
History
DepositionNov 5, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 1, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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: LPXTG cell wall surface protein
B: LPXTG cell wall surface protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4167
Polymers19,1212
Non-polymers2955
Water4,234235
1
A: LPXTG cell wall surface protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,6793
Polymers9,5611
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Methodgel filtration
2
B: LPXTG cell wall surface protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,7384
Polymers9,5611
Non-polymers1773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Methodgel filtration
Unit cell
Length a, b, c (Å)65.380, 47.990, 48.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-1533-

HOH

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Components

#1: Protein LPXTG cell wall surface protein


Mass: 9560.514 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus gordonii (strain Challis / ATCC 35105 / BCRC 15272 / CH1 / DL1 / V288) (bacteria)
Strain: Challis / ATCC 35105 / BCRC 15272 / CH1 / DL1 / V288
Gene: SGO_0707 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A8AW49
#2: Chemical
ChemComp-IS8 / isothiocyanate / Isothiocyanate


Mass: 59.090 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CHNS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 40.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.2 M ammonium sulphate, 150 mM potassium thiocyanate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.78001 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.78001 Å / Relative weight: 1
ReflectionResolution: 0.82→48.38 Å / Num. obs: 147184 / % possible obs: 96.75 % / Redundancy: 2 % / Biso Wilson estimate: 10.86 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.045 / Net I/σ(I): 28.26
Reflection shellResolution: 0.82→0.8493 Å / Redundancy: 1.9 % / Rmerge(I) obs: 2.057 / Mean I/σ(I) obs: 0.34 / Num. unique obs: 24481 / CC1/2: 0.239 / CC star: 0.621 / Rrim(I) all: 2.909 / % possible all: 76.5

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SHIRT R2

Resolution: 0.82→48.38 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 27.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1626 1453 1.01 %
Rwork0.1469 --
obs0.147 144289 96.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 0.82→48.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1283 0 15 235 1533
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0171503
X-RAY DIFFRACTIONf_angle_d1.4912064
X-RAY DIFFRACTIONf_dihedral_angle_d13.915572
X-RAY DIFFRACTIONf_chiral_restr0.102239
X-RAY DIFFRACTIONf_plane_restr0.01268
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.82-0.850.68181150.635811164X-RAY DIFFRACTION76
0.85-0.880.40171460.45214145X-RAY DIFFRACTION97
0.88-0.920.26721460.263314497X-RAY DIFFRACTION99
0.92-0.970.20041490.194614527X-RAY DIFFRACTION99
0.97-1.030.19461470.155514554X-RAY DIFFRACTION99
1.03-1.110.14711440.116814557X-RAY DIFFRACTION99
1.11-1.220.13591480.111414568X-RAY DIFFRACTION99
1.22-1.40.14011500.121514649X-RAY DIFFRACTION99
1.4-1.770.14741500.140414861X-RAY DIFFRACTION100
1.77-48.380.1591580.143215314X-RAY DIFFRACTION100

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