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- PDB-8gr6: Crystal Structure of pilus-specific Sortase C from Streptococcus ... -

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Basic information

Entry
Database: PDB / ID: 8gr6
TitleCrystal Structure of pilus-specific Sortase C from Streptococcus sanguinis
ComponentsSortase-like protein, putative
KeywordsHYDROLASE / Sortase C / Pilus specific sortase / Cysteine-transpeptidase / Streptococcus sanguinis / dental plaque / biofilm
Function / homologySortase C / Sortase family / Sortase domain superfamily / Sortase domain / metal ion binding / membrane / Sortase-like protein, putative
Function and homology information
Biological speciesStreptococcus sanguinis SK36 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsYadav, S. / Parijat, P. / Krishnan, V.
Funding support India, 1items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB)CRG/2019/000432 India
CitationJournal: Int.J.Biol.Macromol. / Year: 2023
Title: Crystal structure of the pilus-specific sortase from early colonizing oral Streptococcus sanguinis captures an active open-lid conformation.
Authors: Yadav, S. / Parijat, P. / Krishnan, V.
History
DepositionSep 1, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Nov 29, 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: Sortase-like protein, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1795
Polymers24,0061
Non-polymers1734
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-24 kcal/mol
Surface area10160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.019, 140.019, 103.625
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-2266-

HOH

21A-2275-

HOH

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Components

#1: Protein Sortase-like protein, putative


Mass: 24005.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sanguinis SK36 (bacteria)
Strain: SK36 / Gene: srtC, SSA_1631 / Variant: No / Plasmid: pET28b / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A3CPB4
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 4.05 Å3/Da / Density % sol: 69 % / Description: Rhombohedral
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100mM Sodium acetate (pH 5.5), 200mM Ammonium-Sulphate and 10% (w/v) PEG 2000 MME and 12.5 mM Zinc-Chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965459 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965459 Å / Relative weight: 1
ReflectionResolution: 2.056→52.331 Å / Num. obs: 23670 / % possible obs: 97.2 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.024 / Rrim(I) all: 0.065 / Net I/σ(I): 13.7
Reflection shellResolution: 2.056→2.092 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1220 / CC1/2: 0.91 / Rpim(I) all: 0.23 / Rrim(I) all: 0.625 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D7W

4d7w


Resolution: 2.06→52.33 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.964 / SU B: 7.232 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.19868 1150 4.9 %RANDOM
Rwork0.17847 ---
obs0.1795 22519 97.21 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.162 Å2
Baniso -1Baniso -2Baniso -3
1--1.18 Å2-0.59 Å2-0 Å2
2---1.18 Å2-0 Å2
3---3.83 Å2
Refinement stepCycle: LAST / Resolution: 2.06→52.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1534 0 7 76 1617
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0171621
X-RAY DIFFRACTIONr_bond_other_d0.0010.0191520
X-RAY DIFFRACTIONr_angle_refined_deg1.4381.8752209
X-RAY DIFFRACTIONr_angle_other_deg1.0692.6973520
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8015209
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.59423.82781
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.24715279
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.251158
X-RAY DIFFRACTIONr_chiral_restr0.0850.2251
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021881
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02340
X-RAY DIFFRACTIONr_mcbond_it2.6083.055821
X-RAY DIFFRACTIONr_mcbond_other2.63.051820
X-RAY DIFFRACTIONr_mcangle_it3.6054.5661035
X-RAY DIFFRACTIONr_mcangle_other3.6044.571036
X-RAY DIFFRACTIONr_scbond_it4.2263.517800
X-RAY DIFFRACTIONr_scbond_other4.2243.517801
X-RAY DIFFRACTIONr_scangle_other5.7355.0951175
X-RAY DIFFRACTIONr_long_range_B_refined8.13237.8111746
X-RAY DIFFRACTIONr_long_range_B_other8.13137.4591731
LS refinement shellResolution: 2.06→2.11 Å
RfactorNum. reflection% reflection
Rfree0.319 78 -
Rwork0.274 1692 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 14.694 Å / Origin y: -15.999 Å / Origin z: -16.597 Å
111213212223313233
T0.1259 Å20.0687 Å20.012 Å2-0.1065 Å20.0022 Å2--0.1314 Å2
L4.6696 °2-0.723 °2-0.9042 °2-2.1863 °20.0546 °2--3.2975 °2
S0.1271 Å °0.509 Å °0.0076 Å °-0.3121 Å °-0.0435 Å °0.1231 Å °0.1757 Å °-0.0033 Å °-0.0836 Å °

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