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- PDB-7bb8: Crystal structure of Lugdulysin, a Staphylococcus lugdunensis M30... -

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Basic information

Entry
Database: PDB / ID: 7bb8
TitleCrystal structure of Lugdulysin, a Staphylococcus lugdunensis M30 zinc metallopeptidase
ComponentsNeutral metalloprotease
KeywordsHYDROLASE / Protease / Virulence factor / peptidase
Function / homologyPeptidase M30, hyicolysin / Peptidase M30 / metallopeptidase activity / proteolysis / metal ion binding / ACETATE ION / CACODYLATE ION / Neutral metalloprotease
Function and homology information
Biological speciesStaphylococcus lugdunensis (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.506 Å
AuthorsRuff, M. / Prevost, G. / Prola, K. / Levy, N.
CitationJournal: To Be Published
Title: Crystal structure of Staphylococcus lugdunensis protease, Lugdulysin
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 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neutral metalloprotease
B: Neutral metalloprotease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,98812
Polymers94,4212
Non-polymers56710
Water16,898938
1
A: Neutral metalloprotease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5336
Polymers47,2101
Non-polymers3235
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Neutral metalloprotease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4556
Polymers47,2101
Non-polymers2455
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)175.590, 68.190, 122.960
Angle α, β, γ (deg.)90.000, 134.190, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Neutral metalloprotease


Mass: 47210.430 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus lugdunensis (bacteria) / Gene: EQ812_06155 / Production host: Staphylococcus lugdunensis (bacteria) / Variant (production host): VISLISI_22 / References: UniProt: A0A292DHH8

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Non-polymers , 5 types, 948 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 938 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.8 Å3/Da / Density % sol: 55.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Sodium Cacodylate pH 6.5; 30% PEG 8000; 0.2 M Sodium acetate

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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 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.506→39.77 Å / Num. obs: 162434 / % possible obs: 95.81 % / Redundancy: 5.4 % / CC1/2: 0.999 / Rrim(I) all: 0.063 / Net I/σ(I): 12.35
Reflection shellResolution: 1.506→1.56 Å / Redundancy: 1.4 % / Num. unique obs: 14979 / CC1/2: 0.264 / % possible all: 62.73

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Processing

Software
NameVersionClassification
PHENIXv1.17refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.506→39.77 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.176 --
Rwork0.156 --
obs-157660 95.8 %
Displacement parametersBiso mean: 31.29 Å2
Refinement stepCycle: LAST / Resolution: 1.506→39.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5838 0 17 945 6800
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00946023
X-RAY DIFFRACTIONf_angle_d0.93978182
X-RAY DIFFRACTIONf_chiral_restr0.0571850
X-RAY DIFFRACTIONf_plane_restr0.00671115
X-RAY DIFFRACTIONf_dihedral_angle_d17.88872230
LS refinement shellResolution: 1.506→1.56 Å / Rfactor Rfree: 0.4157 / Rfactor Rwork: 0.4012

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