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- PDB-8gmx: Crystal structure of pilin-specific sortase SrtC2 from Lactobacil... -

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Basic information

Entry
Database: PDB / ID: 8gmx
TitleCrystal structure of pilin-specific sortase SrtC2 from Lactobacillus rhamnosus GG
ComponentsClass C sortase
KeywordsHYDROLASE / Pilin-specific sortase / cysteine-transpeptidase / pilus assembly / Ligilactobacillus rhamnosus GG / pilus / probiotics
Function / homologySortase C / Sortase family / Sortase domain superfamily / Sortase domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / hydrolase activity / membrane / Sortase
Function and homology information
Biological speciesLacticaseibacillus rhamnosus GG (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsDas, S. / Megta, A.K. / Pratap, S. / Krishnan, V.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR5891/BRB/10/1098/2012 India
CitationJournal: To Be Published
Title: Crystal structure of pilin-specific sortase SrtC2 from Lactobacillus rhamnosus GG
Authors: Das, S. / Megta, A.K. / Pratap, S. / Krishnan, V.
History
DepositionAug 22, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Class C sortase


Theoretical massNumber of molelcules
Total (without water)17,2821
Polymers17,2821
Non-polymers00
Water724
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)80.400, 80.400, 46.895
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Class C sortase / Sortase


Mass: 17282.076 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lacticaseibacillus rhamnosus GG (bacteria)
Strain: ATCC 53103 / LMG 18243 / GG / Gene: GM657_11825, LRHM_2278 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A7S7JH80
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.42 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.05 M Citric acid, 0.05 M BIS-TRIS propane pH 5.0, 16% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873128 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Jun 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873128 Å / Relative weight: 1
ReflectionResolution: 2.604→34.814 Å / Num. obs: 4625 / % possible obs: 83.2 % / Redundancy: 8.1 % / CC1/2: 0.992 / Rpim(I) all: 0.077 / Net I/σ(I): 7.6
Reflection shellResolution: 2.604→2.68 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 231 / CC1/2: 0.415 / Rpim(I) all: 0.61

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CG9

7cg9


Resolution: 2.61→34.81 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2489 242 5.24 %
Rwork0.2048 --
obs0.2075 4620 83.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.61→34.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1069 0 0 4 1073
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021092
X-RAY DIFFRACTIONf_angle_d0.5421489
X-RAY DIFFRACTIONf_dihedral_angle_d5.568155
X-RAY DIFFRACTIONf_chiral_restr0.046179
X-RAY DIFFRACTIONf_plane_restr0.004190
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.61-3.280.33851050.2681952X-RAY DIFFRACTION75
3.28-34.810.22231370.18472426X-RAY DIFFRACTION91

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