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- PDB-9k3g: Crystal structure of Sortase A from Streptococcus pyogenes in com... -

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Basic information

Entry
Database: PDB / ID: 9k3g
TitleCrystal structure of Sortase A from Streptococcus pyogenes in complex with T10
ComponentsSortase
KeywordsHYDROLASE / Inhibitor / Cysteine protease
Function / homologySortase A / Sortase family / Sortase domain superfamily / Sortase domain / cysteine-type peptidase activity / proteolysis / : / Sortase
Function and homology information
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.23 Å
AuthorsYang, C.G. / Gan, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Chemistry / Year: 2025
Title: Structure-Based Development of a Covalent Inhibitor Targeting Streptococcus Pyogenes over Staphylococcus Aureus Sortase A.
Authors: Zhou, H. / Yuan, Z. / Guan, X.N. / Yue, C. / Wu, W. / Lan, L. / Gan, J. / Zhang, T. / Yang, C.G.
History
DepositionOct 18, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release
Revision 1.1May 7, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jun 18, 2025Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sortase
B: Sortase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5809
Polymers41,4992
Non-polymers1,0807
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-22 kcal/mol
Surface area13700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.451, 34.451, 394.345
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Sortase


Mass: 20749.529 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria)
Gene: srtA_2, srtA_1, E0F66_05345, E0F67_00760, FGO82_09960, SAMEA1711581_00311, SAMEA864267_00184
Production host: Escherichia coli (E. coli) / References: UniProt: A0A4U7I1I9
#2: Chemical ChemComp-A1EEN / [4-[[2,4,6-tris(oxidanylidene)-1,3-diazinan-5-ylidene]methyl]phenyl] (2~{S})-4-methyl-2-(phenylmethoxycarbonylamino)pentanoate


Mass: 479.482 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H25N3O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 1.63 Å3/Da / Density % sol: 24.44 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris pH 5.7, 0.2 M Magnesium chloride hexahydrate, 35% (w/v) polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.23→29.84 Å / Num. obs: 79844 / % possible obs: 97.3 % / Redundancy: 16.4 % / CC1/2: 0.997 / Net I/σ(I): 11.1
Reflection shellResolution: 1.23→1.26 Å / Num. unique obs: 4633 / CC1/2: 0.84

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.23→29.84 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.845 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20841 3945 5 %RANDOM
Rwork0.19347 ---
obs0.19419 75697 97.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.915 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20.17 Å20 Å2
2--0.35 Å2-0 Å2
3----1.13 Å2
Refinement stepCycle: 1 / Resolution: 1.23→29.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2348 0 75 266 2689
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0122466
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162314
X-RAY DIFFRACTIONr_angle_refined_deg1.1211.6563339
X-RAY DIFFRACTIONr_angle_other_deg0.3841.5935333
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2045306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg2.28956
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.59510389
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0550.2385
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023016
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02516
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_it0.9411.6311233
X-RAY DIFFRACTIONr_mcbond_other0.9361.6311233
X-RAY DIFFRACTIONr_mcangle_it1.5592.9271538
X-RAY DIFFRACTIONr_mcangle_other1.5582.9271538
X-RAY DIFFRACTIONr_scbond_it1.3411.8181233
X-RAY DIFFRACTIONr_scbond_other1.3411.8181234
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1593.2681802
X-RAY DIFFRACTIONr_long_range_B_refined4.04819.762690
X-RAY DIFFRACTIONr_long_range_B_other3.71817.482619
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.23→1.262 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 209 -
Rwork0.299 4405 -
obs--79.12 %

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