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- PDB-8guu: Crystal structure of pilus-specific sortase C mutant from Strepto... -

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Basic information

Entry
Database: PDB / ID: 8guu
TitleCrystal structure of pilus-specific sortase C mutant from Streptococcus sanguinis
ComponentsSortase-like protein, putative
KeywordsHYDROLASE / Sortase C / pilus-specific sortase / Cysteine transpeptidase / dental plaque / biofilm / pili
Function / homologySortase C / Sortase family / Sortase domain superfamily / Sortase domain / hydrolase activity / membrane / Sortase-like protein, putative
Function and homology information
Biological speciesStreptococcus sanguinis SK36 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.008 Å
AuthorsYadav, S. / Parijat, P.
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 13, 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)21,8133
Polymers21,6881
Non-polymers1242
Water1,56787
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.455, 139.455, 104.692
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-484-

HOH

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Components

#1: Protein Sortase-like protein, putative


Mass: 21688.430 Da / Num. of mol.: 1 / Mutation: C209A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sanguinis SK36 (bacteria)
Strain: SK36 / Gene: srtC, SSA_1631 / Plasmid: pET28b / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A3CPB4
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 4.52 Å3/Da / Density % sol: 69 % / Description: Rhombohedral
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 100 mM Sodium Acetate pH 5.5, 200 mM Ammonium sulphate, and 10 % PEG 2000MME.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 2.008→69.82 Å / Num. obs: 24438 / % possible obs: 93.3 % / Redundancy: 11.8 % / Biso Wilson estimate: 42.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.026 / Net I/σ(I): 15.9
Reflection shellResolution: 2.008→2.043 Å / Redundancy: 9.9 % / Rmerge(I) obs: 1.039 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 12862 / CC1/2: 0.871 / Rpim(I) all: 0.348

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8GR6

8gr6


Resolution: 2.008→69.82 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 8.669 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.119 / 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
Rfree0.21408 1269 5.2 %RANDOM
Rwork0.1832 ---
obs0.1848 23165 93.33 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.637 Å2
Baniso -1Baniso -2Baniso -3
1--1.89 Å2-0.94 Å20 Å2
2---1.89 Å20 Å2
3---6.13 Å2
Refinement stepCycle: LAST / Resolution: 2.008→69.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1523 0 8 87 1618
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0171565
X-RAY DIFFRACTIONr_bond_other_d0.0010.0191488
X-RAY DIFFRACTIONr_angle_refined_deg1.0681.8822124
X-RAY DIFFRACTIONr_angle_other_deg0.9282.6883440
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5855198
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.14723.55376
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.26115269
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.664158
X-RAY DIFFRACTIONr_chiral_restr0.0580.2245
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021775
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02322
X-RAY DIFFRACTIONr_mcbond_it6.0153.317792
X-RAY DIFFRACTIONr_mcbond_other5.9513.313791
X-RAY DIFFRACTIONr_mcangle_it6.684.955990
X-RAY DIFFRACTIONr_mcangle_other6.684.963991
X-RAY DIFFRACTIONr_scbond_it9.6454.02773
X-RAY DIFFRACTIONr_scbond_other9.6414.021774
X-RAY DIFFRACTIONr_scangle_other10.9925.711135
X-RAY DIFFRACTIONr_long_range_B_refined11.84441.5091679
X-RAY DIFFRACTIONr_long_range_B_other11.86141.2921666
LS refinement shellResolution: 2.008→2.06 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 109 -
Rwork0.325 1709 -
obs--94.79 %
Refinement TLS params.Method: refined / Origin x: 14.72 Å / Origin y: -16.008 Å / Origin z: -16.576 Å
111213212223313233
T0.0796 Å20.0372 Å2-0.0038 Å2-0.0491 Å2-0.0075 Å2--0.044 Å2
L5.8838 °2-1.8731 °2-1.2019 °2-2.0661 °20.2372 °2--2.4057 °2
S0.1331 Å °0.3448 Å °-0.2833 Å °-0.2432 Å °-0.0674 Å °0.1877 Å °0.017 Å °-0.0624 Å °-0.0656 Å °

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