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- PDB-7v6k: Crystal structure of Sortase A from Streptococcus pyogenes in com... -

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Basic information

Entry
Database: PDB / ID: 7v6k
TitleCrystal structure of Sortase A from Streptococcus pyogenes in complex with ML346
ComponentsSortase
KeywordsHYDROLASE / Sortase A / transpetidase
Function / homologySortase A / Sortase family / Sortase domain superfamily / Sortase domain / cysteine-type peptidase activity / proteolysis / Chem-5TI / Sortase
Function and homology information
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsYang, C.G. / Gan, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21725801 China
CitationJournal: Rsc Med Chem / Year: 2022
Title: Covalent sortase A inhibitor ML346 prevents Staphylococcus aureus infection of Galleria mellonella.
Authors: Guan, X.N. / Zhang, T. / Yang, T. / Dong, Z. / Yang, S. / Lan, L. / Gan, J. / Yang, C.G.
History
DepositionAug 20, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sortase
B: Sortase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1167
Polymers41,4992
Non-polymers6175
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-13 kcal/mol
Surface area13940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.330, 34.330, 396.230
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 92 and (name N or name...
21(chain B and (resid 92 through 127 or (resid 128...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEULEULEU(chain A and ((resid 92 and (name N or name...AA9232
12LEULEUTHRTHR(chain A and ((resid 92 and (name N or name...AA92 - 24932 - 189
13LEULEUTHRTHR(chain A and ((resid 92 and (name N or name...AA92 - 24932 - 189
14LEULEUTHRTHR(chain A and ((resid 92 and (name N or name...AA92 - 24932 - 189
15LEULEUTHRTHR(chain A and ((resid 92 and (name N or name...AA92 - 24932 - 189
21LEULEUGLUGLU(chain B and (resid 92 through 127 or (resid 128...BB92 - 12732 - 67
22GLUGLUGLUGLU(chain B and (resid 92 through 127 or (resid 128...BB12868
23LEULEUSERSER(chain B and (resid 92 through 127 or (resid 128...BB92 - 24832 - 188
24LEULEUSERSER(chain B and (resid 92 through 127 or (resid 128...BB92 - 24832 - 188
25LEULEUSERSER(chain B and (resid 92 through 127 or (resid 128...BB92 - 24832 - 188
26LEULEUSERSER(chain B and (resid 92 through 127 or (resid 128...BB92 - 24832 - 188

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Components

#1: Protein Sortase / Sortase A / Sortase protein SrtA


Mass: 20749.529 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria)
Gene: srtA, srtA_1, srtA_2, E0F66_05345, E0F67_00760, FGO82_09960, FNL90_04725, FNL91_04720, GQ677_05600, GQR49_04420, GQY31_04460, GQY92_04850, GTK43_04765, GTK52_04270, GTK53_04530, GTK54_03910, ...Gene: srtA, srtA_1, srtA_2, E0F66_05345, E0F67_00760, FGO82_09960, FNL90_04725, FNL91_04720, GQ677_05600, GQR49_04420, GQY31_04460, GQY92_04850, GTK43_04765, GTK52_04270, GTK53_04530, GTK54_03910, GUA39_04435, IB935_04675, IB936_04605, IB937_04535, IB938_05195, KUN2590_09100, KUN4944_08330, MGAS2221_0893, SAMEA1407055_00305, SAMEA1711644_00960, SAMEA3918953_00457, SPNIH34_10200, SPNIH35_09070
Production host: Escherichia coli (E. coli) / References: UniProt: A0A4U7I1I9
#2: Chemical ChemComp-5TI / 5-[3-(4-methoxyphenyl)prop-2-enylidene]-1,3-diazinane-2,4,6-trione


Mass: 272.256 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H12N2O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 1.62 Å3/Da / Density % sol: 24.27 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris pH 5.5, 0.2 M Magnesium chloride hexahydrate, 25% (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: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.57→29.73 Å / Num. obs: 40185 / % possible obs: 99.8 % / Redundancy: 16.4 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 20.7
Reflection shellResolution: 1.57→1.61 Å / Num. unique obs: 40001 / Rpim(I) all: 0.023 / Rrim(I) all: 0.071

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Processing

Software
NameVersionClassification
REFMACv1.0refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FN5

3fn5


Resolution: 1.57→29.005 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.223 2051 5.13 %
Rwork0.19 --
obs0.1918 40001 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.47 Å2 / Biso mean: 29.904 Å2 / Biso min: 14.19 Å2
Refinement stepCycle: final / Resolution: 1.57→29.005 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2406 0 43 120 2569
Biso mean--49.34 36.79 -
Num. residues----315
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1418X-RAY DIFFRACTION9.202TORSIONAL
12B1418X-RAY DIFFRACTION9.202TORSIONAL
LS refinement shellResolution: 1.57→1.6065 Å
RfactorNum. reflection
Rfree0.3207 136
Rwork0.2623 -
obs-2387
Refinement TLS params.Method: refined / Origin x: 18.0361 Å / Origin y: 1.2371 Å / Origin z: 33.5393 Å
111213212223313233
T0.2068 Å20.028 Å2-0.0142 Å2-0.1216 Å20.0048 Å2--0.1924 Å2
L0.3945 °20.0745 °2-0.2938 °2-0.3664 °2-0.3056 °2--2.4215 °2
S-0.0245 Å °0.0448 Å °0.0109 Å °-0.0568 Å °0.043 Å °0.0305 Å °0.035 Å °-0.058 Å °-0.0195 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA92 - 249
2X-RAY DIFFRACTION1allB92 - 248

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