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- PDB-5l2d: Streptococcal surface adhesin - CshA NR2 -

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Basic information

Entry
Database: PDB / ID: 5l2d
TitleStreptococcal surface adhesin - CshA NR2
ComponentsSurface-associated protein CshA
KeywordsCELL ADHESION / Streptococcus / adhesin
Function / homology
Function and homology information


extracellular region
Similarity search - Function
CshA domain / GEVED domain / Surface adhesin CshA repetitive domain / GEVED domain / 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
Surface-associated protein CshA
Similarity search - Component
Biological speciesStreptococcus gordonii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.66 Å
AuthorsBack, C.R. / Race, P.R. / Jenkinson, H.F.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: The Streptococcus gordonii Adhesin CshA Protein Binds Host Fibronectin via a Catch-Clamp Mechanism.
Authors: Back, C.R. / Sztukowska, M.N. / Till, M. / Lamont, R.J. / Jenkinson, H.F. / Nobbs, A.H. / Race, P.R.
History
DepositionAug 1, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2017Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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-associated protein CshA
B: Surface-associated protein CshA
C: Surface-associated protein CshA
D: Surface-associated protein CshA


Theoretical massNumber of molelcules
Total (without water)147,1044
Polymers147,1044
Non-polymers00
Water362
1
A: Surface-associated protein CshA
C: Surface-associated protein CshA


Theoretical massNumber of molelcules
Total (without water)73,5522
Polymers73,5522
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-33 kcal/mol
Surface area11060 Å2
MethodPISA
2
B: Surface-associated protein CshA
D: Surface-associated protein CshA


Theoretical massNumber of molelcules
Total (without water)73,5522
Polymers73,5522
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-30 kcal/mol
Surface area11540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.929, 173.929, 104.071
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein
Surface-associated protein CshA


Mass: 36776.012 Da / Num. of mol.: 4 / Fragment: UNP residues 223-540
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: cshA, SGO_0854 / Production host: Escherichia coli (E. coli) / References: UniProt: A8AWJ3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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
Method details: The structure of CshA-NR2 was initially determined in space group P6222, with two molecules in the asymmetric unit, to 3.5 A resolution by the single wavelength anomalous dispersion ...Method details: The structure of CshA-NR2 was initially determined in space group P6222, with two molecules in the asymmetric unit, to 3.5 A resolution by the single wavelength anomalous dispersion (SAD) method as applied to selonomethionine (SeMet) labeled crystals of dimeric CshA-NR2. Identification of heavy atom sites and the resulting initial phase calculation was carried out, employing diffraction data collected from two different crystals of SeMet labeled dimeric CshA-NR2, which were merged together. The software located 18 Se sites. The output model was refined and used as a molecular replacement search model to elucidate a higher resolution CshA-NR2 structure (2.7 A), employing diffraction data collected from a crystal of unlabeled CshA-NR2 (also in space group P6222).

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Sample preparation

Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Na/K tartrate, MMT buffer [DL-malic acid, MES and Tris base in the molar ratios 1:2:2] (pH 5.0), 22% PEG 3350.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.66→61.01 Å / Num. obs: 27284 / % possible obs: 100 % / Redundancy: 16.8 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 19.8
Reflection shellResolution: 2.66→2.8 Å / Redundancy: 16.6 % / Rmerge(I) obs: 1.477 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.66→61.01 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.918 / SU B: 11.993 / SU ML: 0.234 / Cross valid method: THROUGHOUT / ESU R: 0.309 / ESU R Free: 0.267 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26353 1368 5 %RANDOM
Rwork0.20131 ---
obs0.20435 25890 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.933 Å2
Baniso -1Baniso -2Baniso -3
1--1.21 Å2-0.6 Å20 Å2
2---1.21 Å20 Å2
3---3.92 Å2
Refinement stepCycle: LAST / Resolution: 2.66→61.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3647 0 0 2 3649
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.023736
X-RAY DIFFRACTIONr_bond_other_d0.0010.023433
X-RAY DIFFRACTIONr_angle_refined_deg1.8261.9595093
X-RAY DIFFRACTIONr_angle_other_deg0.86737921
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5765479
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.81425.108139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.14315557
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.241157
X-RAY DIFFRACTIONr_chiral_restr0.0950.2575
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214219
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02788
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_it5.4796.6551940
X-RAY DIFFRACTIONr_mcbond_other5.4296.6531939
X-RAY DIFFRACTIONr_mcangle_it8.1079.9592411
X-RAY DIFFRACTIONr_mcangle_other8.1069.9632412
X-RAY DIFFRACTIONr_scbond_it5.8676.9841796
X-RAY DIFFRACTIONr_scbond_other5.8666.9871797
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.76110.282683
X-RAY DIFFRACTIONr_long_range_B_refined11.39753.944068
X-RAY DIFFRACTIONr_long_range_B_other11.39653.964069
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.656→2.725 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 102 -
Rwork0.367 1867 -
obs--100 %

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