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- PDB-7bb9: Crystal structure of Lugdulysin E242Q Y315F mutant -

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Basic information

Entry
Database: PDB / ID: 7bb9
TitleCrystal structure of Lugdulysin E242Q Y315F mutant
ComponentsLugdulysin E242Q Y315F
KeywordsHYDROLASE / Protease / peptidase / virulence factor
Function / homologyPeptidase M30, hyicolysin / Peptidase M30 / metallopeptidase activity / proteolysis / Neutral metalloprotease
Function and homology information
Biological speciesStaphylococcus lugdunensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsRuff, M. / Prevost, G. / Prola, K. / Levy, N.
CitationJournal: To Be Published
Title: Crystal structure of Lugdulysin E242Q Y315F mutant
Authors: Ruff, M. / Prevost, G. / Prola, K. / Levy, N.
History
DepositionDec 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lugdulysin E242Q Y315F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3795
Polymers47,1931
Non-polymers1864
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-38 kcal/mol
Surface area17060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.250, 96.250, 84.170
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Space group name HallP4ab2ab
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z
#3: y+1/2,-x+1/2,z
#4: x+1/2,-y+1/2,-z
#5: -x+1/2,y+1/2,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z

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Components

#1: Protein Lugdulysin E242Q Y315F


Mass: 47193.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus lugdunensis (bacteria) / Gene: EQ812_06155 / Production host: Escherichia coli (E. coli) / Variant (production host): wk6 / References: UniProt: A0A292DHH8
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 304 / 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: 2.07 Å3/Da / Density % sol: 40.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: 0.1 M Tris-Bicine pH 8.5; 12.5% v/v MPD; 12.5% PEG 1000; 12.5% w/v PEG 3350; 30 mM Magnesium chloride hexahydrate; 30 mM Calcium chloride dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.5418 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Jul 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.967→42.08 Å / Num. obs: 28567 / % possible obs: 99.3 % / Redundancy: 19 % / CC1/2: 0.991 / Net I/σ(I): 6.13
Reflection shellResolution: 1.967→2.037 Å / Num. unique obs: 2679 / CC1/2: 0.307 / % possible all: 93.66

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Processing

Software
NameVersionClassification
PHENIXv1.17refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7BB8

7bb8


Resolution: 1.97→42.08 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.24 1995 -
Rwork0.19 --
obs-28497 99.3 %
Displacement parametersBiso mean: 28.96 Å2
Refinement stepCycle: LAST / Resolution: 1.97→42.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3234 0 4 304 3542
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00743309
X-RAY DIFFRACTIONf_angle_d0.80494479
X-RAY DIFFRACTIONf_chiral_restr0.0536462
X-RAY DIFFRACTIONf_plane_restr0.005609
X-RAY DIFFRACTIONf_dihedral_angle_d20.4871244
LS refinement shellResolution: 1.97→2.037 Å /
RfactorNum. reflection
Rfree0.3535 183
Rwork0.3196 -

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