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- PDB-7f87: Crystal structure of housekeeping sortase SrtA bound with self de... -

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Basic information

Entry
Database: PDB / ID: 7f87
TitleCrystal structure of housekeeping sortase SrtA bound with self derived tripeptide from Lactobacillus rhamnosus GG
Components
  • Class A sortase
  • Self Derived Peptide
KeywordsTRANSFERASE / housekeeping sortase / cysteine-transpeptidase / pilus assembly / lactobacillar pilus / SpaCBA pilus / SpaFED pilus / HYDROLASE / probiotics / SrtA
Function / homologySortase A / Sortase family / Sortase domain superfamily / Sortase domain / cysteine-type peptidase activity / proteolysis / PHOSPHATE ION / Class A sortase
Function and homology information
Biological speciesLactobacillus rhamnosus (bacteria)
Lacticaseibacillus rhamnosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsPratap, 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 housekeeping sortase SrtA bound with self derived tripeptide from Lactobacillus rhamnosus GG
Authors: Pratap, S. / Krishnan, V.
History
DepositionJul 1, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 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: Class A sortase
B: Class A sortase
F: Self Derived Peptide
G: Self Derived Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,69310
Polymers33,1564
Non-polymers5376
Water2,900161
1
A: Class A sortase
F: Self Derived Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8635
Polymers16,5782
Non-polymers2853
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Class A sortase
G: Self Derived Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8305
Polymers16,5782
Non-polymers2523
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.608, 55.674, 75.312
Angle α, β, γ (deg.)90.00, 103.22, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Class A sortase / Sortase


Mass: 16274.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus rhamnosus (bacteria)
Gene: F5976_12260, F8M46_11135, FEZ43_04140, GKD16_09085, HWN39_00700, LRHP540_01088, PY91_04000
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0E3D3H8
#2: Protein/peptide Self Derived Peptide


Mass: 303.355 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lacticaseibacillus rhamnosus (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: PO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.13 Å3/Da / Density % sol: 42.26 % / Description: Plate-like
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.05 M Citric Bis-Tris Propane, pH 5.0 and 16% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97934 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.686→73.32 Å / Num. obs: 23044 / % possible obs: 90 % / Redundancy: 3.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.061 / Net I/σ(I): 9.9
Reflection shellResolution: 1.686→1.865 Å / Rmerge(I) obs: 1.151 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1153 / CC1/2: 0.476 / Rpim(I) all: 0.674

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FN5

3fn5


Resolution: 1.69→73.32 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.8 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21368 1135 4.9 %RANDOM
Rwork0.18139 ---
obs0.18307 21908 73 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.939 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å2-0 Å2-0.03 Å2
2---0.04 Å2-0 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.69→73.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2252 0 29 161 2442
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0182305
X-RAY DIFFRACTIONr_bond_other_d0.0010.022323
X-RAY DIFFRACTIONr_angle_refined_deg1.3151.893114
X-RAY DIFFRACTIONr_angle_other_deg0.9992.8385355
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7885292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.49626.66784
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.29215438
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.184152
X-RAY DIFFRACTIONr_chiral_restr0.0720.2380
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022526
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02446
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_it3.0672.2061180
X-RAY DIFFRACTIONr_mcbond_other3.0572.2041179
X-RAY DIFFRACTIONr_mcangle_it4.4343.2711468
X-RAY DIFFRACTIONr_mcangle_other4.4333.2731469
X-RAY DIFFRACTIONr_scbond_it4.9962.8131125
X-RAY DIFFRACTIONr_scbond_other4.9942.8151126
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.4333.9861647
X-RAY DIFFRACTIONr_long_range_B_refined9.21128.0752465
X-RAY DIFFRACTIONr_long_range_B_other9.18627.8312434
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.69→1.73 Å
RfactorNum. reflection% reflection
Rfree0.367 9 -
Rwork0.358 78 -
obs--3.67 %

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