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- PDB-7avh: Streptococcal High Identity Repeats in Tandem (SHIRT) domains 3-4... -

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Basic information

Entry
Database: PDB / ID: 7avh
TitleStreptococcal High Identity Repeats in Tandem (SHIRT) domains 3-4 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


extracellular region / membrane
Similarity search - Function
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
LPXTG cell wall surface protein
Similarity search - Component
Biological speciesStreptococcus gordonii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsWhelan, 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: 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

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Assembly

Deposited unit
A: LPXTG cell wall surface protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5374
Polymers18,2571
Non-polymers2803
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area500 Å2
ΔGint-7 kcal/mol
Surface area10340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.127, 37.155, 101.140
Angle α, β, γ (deg.)90.00, 95.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein LPXTG cell wall surface protein


Mass: 18256.844 Da / Num. of mol.: 1
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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.4 Å3/Da / Density % sol: 48.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 65% MPD, 0.1 M Tris pH 8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 3, 2015
RadiationMonochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.35→34.88 Å / Num. obs: 39416 / % possible obs: 99.9 % / Redundancy: 4 % / Biso Wilson estimate: 10.8 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.066 / Net I/σ(I): 8.9
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.96 / Num. unique obs: 1911 / CC1/2: 0.562 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.5.26data scaling
PDB_EXTRACT3.2data extraction
XDSOctober 15, 2015data reduction
PHASER2.5.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Shirt R3

Resolution: 1.35→34.85 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.972 / SU B: 2.266 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.049 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17027 1892 4.8 %RANDOM
Rwork0.13385 ---
obs0.1357 37511 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.017 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å2-0.12 Å2
2---0.21 Å20 Å2
3---0.5 Å2
Refinement stepCycle: 1 / Resolution: 1.35→34.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1288 0 17 195 1500
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0131491
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171330
X-RAY DIFFRACTIONr_angle_refined_deg2.1171.6752063
X-RAY DIFFRACTIONr_angle_other_deg1.6181.5893149
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4625204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.79126.72161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.5615240
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0960.2208
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021713
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02287
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1061.766738
X-RAY DIFFRACTIONr_mcbond_other2.0931.762733
X-RAY DIFFRACTIONr_scbond_it4.3871.898753
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1612.6961118
X-RAY DIFFRACTIONr_rigid_bond_restr6.47131486
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 135 -
Rwork0.224 2745 -
obs--99.65 %

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