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- PDB-5go6: Structure of sortase E T196V mutant from Streptomyces avermitilis -

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Basic information

Entry
Database: PDB / ID: 5go6
TitleStructure of sortase E T196V mutant from Streptomyces avermitilis
ComponentsPutative secreted proteinSecretory protein
KeywordsHYDROLASE / beta barrel / sortase-fold / cysteine transpeptidase / T196V mutant
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
Biological speciesStreptomyces avermitilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsDas, S. / Pawale, V.S. / Dadireddy, V. / Roy, R.P. / Ramakumar, S.
CitationJournal: To Be Published
Title: Structure of sortase E T196V mutant from Streptomyces avermitilis
Authors: Das, S. / Pawale, V.S. / Dadireddy, V. / Roy, R.P. / Ramakumar, S.
History
DepositionJul 26, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative secreted protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5183
Polymers22,3261
Non-polymers1922
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area310 Å2
ΔGint-21 kcal/mol
Surface area7680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.983, 84.983, 48.005
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 Putative secreted protein / Secretory protein / Sortase E


Mass: 22326.262 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 51-230 / Mutation: T196V
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-CodonPlus-RP / References: UniProt: Q82FC3
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.25 Å3/Da / Density % sol: 45.25 %
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: Apr 15, 2015 / Details: bent collimating mirror and toroid
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 22502 / % possible obs: 99.9 % / Redundancy: 12.2 % / Biso Wilson estimate: 34 Å2 / CC1/2: 0.982 / Rmerge(I) obs: 0.065 / Net I/σ(I): 39.1
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 10.7 % / Mean I/σ(I) obs: 2.77 / CC1/2: 0.877 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GO5

5go5


Resolution: 1.7→50.01 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.783 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.206 1106 5 %RANDOM
Rwork0.17277 ---
obs0.17435 21161 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.081 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20.33 Å2-0 Å2
2--0.66 Å20 Å2
3----2.13 Å2
Refinement stepCycle: LAST / Resolution: 1.7→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1187 0 10 98 1295
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191246
X-RAY DIFFRACTIONr_bond_other_d0.0020.021168
X-RAY DIFFRACTIONr_angle_refined_deg1.8951.9621698
X-RAY DIFFRACTIONr_angle_other_deg0.98932689
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4055152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.35322.03754
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.43415195
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3451510
X-RAY DIFFRACTIONr_chiral_restr0.1110.2184
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211375
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02293
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_it2.852.906602
X-RAY DIFFRACTIONr_mcbond_other2.7792.9601
X-RAY DIFFRACTIONr_mcangle_it3.9064.329750
X-RAY DIFFRACTIONr_mcangle_other3.9044.335751
X-RAY DIFFRACTIONr_scbond_it4.3013.49644
X-RAY DIFFRACTIONr_scbond_other4.2273.464637
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.424.961935
X-RAY DIFFRACTIONr_long_range_B_refined8.30335.5181386
X-RAY DIFFRACTIONr_long_range_B_other8.16434.6891350
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 80 -
Rwork0.22 1548 -
obs--99.94 %

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