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- PDB-5cuw: Crystal structure of Sortase E1 from Streptomyces coelicolor with... -

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Basic information

Entry
Database: PDB / ID: 5cuw
TitleCrystal structure of Sortase E1 from Streptomyces coelicolor with tripeptide in the active site
ComponentsSrtE1
KeywordsMEMBRANE PROTEIN / sortase / class E / SrtE / transpeptidase / aminoacyltransferase / cysteine endopeptidase / bacterial protein / protein binding / catalytic domain / beta barrel
Function / homology
Function and homology information


sortase A / peptidase activity / membrane => GO:0016020 / plasma membrane
Similarity search - Function
Sortase E / Sortase; Chain: A; / Sortase / Sortase family / Sortase domain superfamily / Sortase domain / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.887 Å
AuthorsKattke, M.D. / Cascio, D. / Sawaya, M.R. / Clubb, R.T.
CitationJournal: To be published
Title: Crystal structure of the first class E sortase transpeptidase, SrtE1 from Streptomyces coelicolor
Authors: Kattke, M.D. / Cascio, D. / Sawaya, M.R. / Elliot, M.A. / Clubb, R.T.
History
DepositionJul 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_prerelease_seq / pdbx_struct_oper_list / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SrtE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3412
Polymers21,2491
Non-polymers921
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.110, 104.300, 79.020
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-537-

HOH

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Components

#1: Protein SrtE1 / Putative integral membrane protein


Mass: 21249.221 Da / Num. of mol.: 1 / Fragment: UNP residues 162-352
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145) (bacteria)
Strain: ATCC BAA-471 / A3(2) / M145 / Gene: SCO3850 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9XA14
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Fragment: GOL / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.57 Å3/Da / Density % sol: 52.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 50 mM HEPES, pH 7.5, 1.4 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.88→43.53 Å / Num. obs: 17717 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 26.16 Å2 / Rmerge F obs: 0.987 / Rmerge(I) obs: 0.189 / Rrim(I) all: 0.207 / Χ2: 1.059 / Net I/σ(I): 6.82 / Num. measured all: 104280
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.88-1.930.651.1081.38355713269161.26269.1
1.93-1.980.7710.83826091129012890.93999.9
1.98-2.040.8310.6762.465794125712510.7699.5
2.04-2.10.8160.5942.865567122312110.6799
2.1-2.170.8880.5113.184972118611730.58198.9
2.17-2.250.9040.5823.936742115211450.63699.4
2.25-2.330.9250.5554.677693111211100.699.8
2.33-2.430.940.4575.377284106510630.49699.8
2.43-2.540.9530.4155.986866101510140.4599.9
2.54-2.660.9490.3516.69688510019980.38199.7
2.66-2.810.9640.2877.3160829399370.31299.8
2.81-2.980.9770.258.5760678918910.271100
2.98-3.180.9770.20110.4956758268250.21899.9
3.18-3.440.9550.15912.153427947930.17399.9
3.44-3.760.9790.13413.6346987167140.14699.7
3.76-4.210.9880.11614.0739286656550.12898.5
4.21-4.860.9850.09315.6537795895880.10299.8
4.86-5.950.9880.09115.6234355125120.099100
5.95-8.420.9890.08415.0724193973930.09399
8.420.9910.08215.6914042452390.0997.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.99 Å47.32 Å
Translation1.99 Å47.32 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.5.6phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.887→43.526 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.32 / Phase error: 26.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2273 879 5 %
Rwork0.1998 16698 -
obs0.2013 17577 97.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.74 Å2 / Biso mean: 33.7971 Å2 / Biso min: 15.57 Å2
Refinement stepCycle: final / Resolution: 1.887→43.526 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1213 0 14 37 1264
Biso mean--98.6 33.84 -
Num. residues----162
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071271
X-RAY DIFFRACTIONf_angle_d1.0891728
X-RAY DIFFRACTIONf_chiral_restr0.046192
X-RAY DIFFRACTIONf_plane_restr0.005223
X-RAY DIFFRACTIONf_dihedral_angle_d12.007474
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8871-2.00530.34461310.33922501263289
2.0053-2.16010.30811470.2552785293299
2.1601-2.37750.25621480.2222813296199
2.3775-2.72150.26821490.20662827297699
2.7215-3.42860.2381500.18892848299899
3.4286-43.53730.17191540.16772924307898
Refinement TLS params.Method: refined / Origin x: -6.6234 Å / Origin y: -20.9557 Å / Origin z: 6.0701 Å
111213212223313233
T0.1755 Å2-0.0146 Å20.0026 Å2-0.2502 Å20.0122 Å2--0.1759 Å2
L2.1046 °2-0.1137 °20.0383 °2-1.7581 °20.2268 °2--1.5328 °2
S0.0425 Å °0.1492 Å °-0.0475 Å °-0.0584 Å °0.0153 Å °0.0488 Å °0.0084 Å °-0.098 Å °-0.0524 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA168 - 351
2X-RAY DIFFRACTION1allB1 - 38
3X-RAY DIFFRACTION1allC1

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