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- PDB-9j0t: Crystal Structure of Sortase E mutant - C222A from Thermobifida fusca -

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Basic information

Entry
Database: PDB / ID: 9j0t
TitleCrystal Structure of Sortase E mutant - C222A from Thermobifida fusca
ComponentsPeptidase C60, sortase A and B
KeywordsHYDROLASE / Enzyme catalysis / Sortase E / Substrate specificity / Transpeptidase / Thermobifida fusca / sorting motif / SrtE
Function / homologySortase E / : / Sortase family / Sortase domain superfamily / Sortase domain / membrane / Peptidase C60, sortase A and B
Function and homology information
Biological speciesThermobifida fusca YX (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSharma, V. / Murmu, S. / Roy, R.P. / Krishnan, V.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India) India
CitationJournal: To Be Published
Title: Crystal Structure of Sortase E mutant - C222A from Thermobifida fusca
Authors: Sharma, V. / Murmu, S. / Roy, R.P. / Krishnan, V.
History
DepositionAug 2, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidase C60, sortase A and B
B: Peptidase C60, sortase A and B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,94011
Polymers40,4992
Non-polymers4419
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-29 kcal/mol
Surface area16350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.939, 111.939, 71.638
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Peptidase C60, sortase A and B / Peptidase C60 / sortase E


Mass: 20249.443 Da / Num. of mol.: 2 / Mutation: C222A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobifida fusca YX (bacteria) / Strain: YX / Gene: Tfu_2383 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q47MA6
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.91 Å3/Da / Density % sol: 57.69 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 1.5M Lithium sulfate, 0.1M HEPES-NaOH, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.885603 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Apr 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.885603 Å / Relative weight: 1
ReflectionResolution: 1.5→41.03 Å / Num. obs: 48207 / % possible obs: 92.8 % / Redundancy: 4.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.034 / Rrim(I) all: 0.075 / Net I/σ(I): 9.4
Reflection shellResolution: 1.5→1.57 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2410 / CC1/2: 0.807 / Rpim(I) all: 0.223 / Rrim(I) all: 0.509 / % possible all: 80.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→41.03 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.885 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17905 2495 5.2 %RANDOM
Rwork0.1437 ---
obs0.14556 45710 68.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.822 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å2-0 Å2-0 Å2
2--0.19 Å2-0 Å2
3----0.38 Å2
Refinement stepCycle: 1 / Resolution: 1.5→41.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2712 0 27 267 3006
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0122826
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162553
X-RAY DIFFRACTIONr_angle_refined_deg1.6741.8473856
X-RAY DIFFRACTIONr_angle_other_deg0.5631.7375937
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7485350
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.3359
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.11410411
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0890.2412
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023303
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02565
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_it4.6511.8511394
X-RAY DIFFRACTIONr_mcbond_other4.6411.8511394
X-RAY DIFFRACTIONr_mcangle_it6.9683.3291740
X-RAY DIFFRACTIONr_mcangle_other6.9673.331741
X-RAY DIFFRACTIONr_scbond_it6.9352.1631432
X-RAY DIFFRACTIONr_scbond_other6.9352.1631433
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.0743.8112115
X-RAY DIFFRACTIONr_long_range_B_refined12.63422.9911311
X-RAY DIFFRACTIONr_long_range_B_other12.39722.811254
X-RAY DIFFRACTIONr_rigid_bond_restr3.65635379
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.501→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 58 -
Rwork0.279 1112 -
obs--22.63 %

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