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- PDB-6u2a: ShyA endopeptidase from Vibrio cholera (open form) -

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Basic information

Entry
Database: PDB / ID: 6u2a
TitleShyA endopeptidase from Vibrio cholera (open form)
ComponentsShyA endopeptidase
KeywordsHYDROLASE / M23 peptidase / peptidoglycan / crosslinks / periplasm
Function / homology
Function and homology information


lysostaphin / peptidoglycan binding / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metalloendopeptidase activity / periplasmic space / hydrolase activity / metal ion binding / plasma membrane
Similarity search - Function
Opacity-associated protein A / Opacity-associated protein A LysM-like domain / Csd3-like, second N-terminal domain / Csd3 second domain / : / Peptidase M23 / Peptidase family M23 / Duplicated hybrid motif
Similarity search - Domain/homology
Cell wall endopeptidase family M23/M37 / Peptidoglycan DD-endopeptidase ShyA
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSaper, M.A. / Kelley, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Structural basis of peptidoglycan endopeptidase regulation.
Authors: Shin, J.H. / Sulpizio, A.G. / Kelley, A. / Alvarez, L. / Murphy, S.G. / Fan, L. / Cava, F. / Mao, Y. / Saper, M.A. / Dorr, T.
History
DepositionAug 19, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2020Group: 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 1.2Oct 11, 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 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ShyA endopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6902
Polymers45,6251
Non-polymers651
Water18010
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.272, 82.492, 82.522
Angle α, β, γ (deg.)90.000, 102.692, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y

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Components

#1: Protein ShyA endopeptidase


Mass: 45624.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: ShyA / Plasmid: pET28-VcShyA-His6
Details (production host): Full-length ShyA followed by His6
Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami 2(DE3)
References: UniProt: A0A0H6MKE7, UniProt: Q9KN86*PLUS, lysostaphin
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.74 Å3/Da / Density % sol: 59.9 % / Description: elongated prisms
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Protein (0.5 microliter): 18 mg/ml in 20 mM Tris-HCl, 150 mM NaCl pH 7.6 Precipitant (0.5 microliter): 0.25 M sodium citrate, 10% polyethylene glycol 3350, 0.1 M Tris-HCl pH 6.0
PH range: 6-7.5

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Data collection

DiffractionMean temperature: 125 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.07811 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07811 Å / Relative weight: 1
ReflectionResolution: 2.025→54.9 Å / Num. obs: 17391 / % possible obs: 54.1 % / Redundancy: 7 % / Biso Wilson estimate: 60.31 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.011 / Rrim(I) all: 0.059 / Net I/σ(I): 9.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.026-2.2766.21.131.68700.5490.4871.23466.7
6.143-54.8496.40.04119.48690.9960.0170.04573.3

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Processing

Software
NameVersionClassification
PHENIXdev_3580refinement
PHASER2.8.2phasing
PDB_EXTRACT3.25data extraction
STARANISO1.0.5data scaling
autoPROC1.0.5data scaling
XDSJan 26, 2018data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GUI

2gui


Resolution: 2.3→36.58 Å / SU ML: 0.2891 / Cross valid method: FREE R-VALUE / Phase error: 38.328
RfactorNum. reflection% reflectionSelection details
Rfree0.2936 842 5.15 %Random
Rwork0.2538 ---
obs-16347 74.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 78.09 Å2
Refine analyzeLuzzati d res low obs: 40 Å
Refinement stepCycle: LAST / Resolution: 2.3→36.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2852 0 1 10 2863
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00342911
X-RAY DIFFRACTIONf_angle_d0.6353929
X-RAY DIFFRACTIONf_chiral_restr0.0473424
X-RAY DIFFRACTIONf_plane_restr0.0033513
X-RAY DIFFRACTIONf_dihedral_angle_d14.7361760
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.440.4496740.36951172X-RAY DIFFRACTION34.07
2.44-2.630.3936890.36851816X-RAY DIFFRACTION52.65
2.63-2.90.35951470.35612560X-RAY DIFFRACTION74.04
2.9-3.320.36211890.32873368X-RAY DIFFRACTION97
3.32-4.180.27381630.24763404X-RAY DIFFRACTION97.75
4.18-36.580.25641800.21073185X-RAY DIFFRACTION90.46

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