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- PDB-5go5: Structure of sortase E from Streptomyces avermitilis -

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Basic information

Entry
Database: PDB / ID: 5go5
TitleStructure of sortase E from Streptomyces avermitilis
Componentssortase
KeywordsHYDROLASE / beta barrel / sortase-fold / cysteine transpeptidase
Function / homology
Function and homology information


hydrolase activity / 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
GLYCINE / Secreted protein
Similarity search - Component
Biological speciesStreptomyces avermitilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsDas, S. / Pawale, V.S. / Dadireddy, V. / Roy, R.P. / Ramakumar, S.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structure and specificity of a new class of Ca2+-independent housekeeping sortase from Streptomyces avermitilis provide insights into its non-canonical substrate preference.
Authors: Das, S. / Pawale, V.S. / Dadireddy, V. / Singh, A.K. / Ramakumar, S. / Roy, R.P.
History
DepositionJul 26, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: sortase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6724
Polymers22,4041
Non-polymers2673
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint-18 kcal/mol
Surface area7560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.840, 85.840, 48.200
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 sortase / Sortase E


Mass: 22404.352 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 51-230
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avermitilis (strain ATCC 31267 / DSM 46492 / JCM 5070 / NBRC 14893 / NCIMB 12804 / NRRL 8165 / MA-4680) (bacteria)
Strain: ATCC 31267 / DSM 46492 / JCM 5070 / NBRC 14893 / NCIMB 12804 / NRRL 8165 / MA-4680
Gene: SAVERM_4333 / Plasmid: pET28b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS / References: UniProt: Q82FC3
#2: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.3 Å3/Da / Density % sol: 46.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.75 / Details: 1.6M ammonium sulfate, 0.1M citric acid pH 3.75

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 5, 2014 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.65→42.92 Å / Num. obs: 24903 / % possible obs: 99.9 % / Redundancy: 9.3 % / Biso Wilson estimate: 26.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Net I/σ(I): 19.3
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.778 / Mean I/σ(I) obs: 3.3 / CC1/2: 0.808 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RCC

3rcc


Resolution: 1.65→42.92 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.343 / SU ML: 0.046 / Cross valid method: FREE R-VALUE / ESU R: 0.074 / ESU R Free: 0.077 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19078 1243 5 %RANDOM
Rwork0.16124 ---
obs0.16272 23644 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.39 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20.09 Å2-0 Å2
2--0.18 Å20 Å2
3----0.59 Å2
Refinement stepCycle: 1 / Resolution: 1.65→42.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1197 0 15 154 1366
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191245
X-RAY DIFFRACTIONr_bond_other_d0.0020.021140
X-RAY DIFFRACTIONr_angle_refined_deg1.581.9661695
X-RAY DIFFRACTIONr_angle_other_deg0.98532624
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2375150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.89622.552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.9415184
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.685158
X-RAY DIFFRACTIONr_chiral_restr0.0930.2184
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211370
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02284
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_it1.6161.773609
X-RAY DIFFRACTIONr_mcbond_other1.5831.77608
X-RAY DIFFRACTIONr_mcangle_it2.4352.632756
X-RAY DIFFRACTIONr_mcangle_other2.4352.637757
X-RAY DIFFRACTIONr_scbond_it2.4122.12636
X-RAY DIFFRACTIONr_scbond_other2.3962.073628
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7172.99928
X-RAY DIFFRACTIONr_long_range_B_refined6.19623.7651480
X-RAY DIFFRACTIONr_long_range_B_other5.84322.1611397
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 100 -
Rwork0.219 1706 -
obs--99.23 %

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