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- PDB-8af1: Beta-Lytic Protease from Lysobacter capsici -

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Basic information

Entry
Database: PDB / ID: 8af1
TitleBeta-Lytic Protease from Lysobacter capsici
ComponentsPeptidase M23
KeywordsHYDROLASE / ELASTASE / PEPTIDOGLYCAN / Beta-lytic protease / antimicrobial activity / Lysobacter / Metalloprotease
Function / homologyPeptidase M23A, B-lytic metalloendopeptidase / Duplicated hybrid motif / metalloendopeptidase activity / proteolysis / FORMIC ACID / Peptidase M23
Function and homology information
Biological speciesLysobacter capsici (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsGabdulkhakov, A.G. / Tishchenko, T.V. / Kudryakova, I.V. / Afoshin, A.S. / Vasilyeva, N.V.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Foundation for Basic Research18-02-40008 Russian Federation
CitationJournal: Int J Mol Sci / Year: 2022
Title: Structural and Functional Characterization of beta-lytic Protease from Lysobacter capsici VKM B-2533 T.
Authors: Afoshin, A. / Tishchenko, S. / Gabdulkhakov, A. / Kudryakova, I. / Galemina, I. / Zelenov, D. / Leontyevskaya, E. / Saharova, S. / Leontyevskaya Vasilyeva, N.
History
DepositionJul 15, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidase M23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5536
Polymers19,2221
Non-polymers3315
Water2,684149
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)70.580, 44.130, 52.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-361-

HOH

21A-388-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Peptidase M23


Mass: 19221.842 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: VKM B-2533T / Source: (gene. exp.) Lysobacter capsici (bacteria) / Gene: CNO08_04090 / Production host: Lysobacter capsici (bacteria) / References: UniProt: A0A290ZX82

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Non-polymers , 5 types, 154 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.13 Å3/Da / Density % sol: 42.39 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 400 mM NaCl, 30 mM Na-acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.003185 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.003185 Å / Relative weight: 1
ReflectionResolution: 1.57→45 Å / Num. obs: 23631 / % possible obs: 100 % / Redundancy: 12.5 % / Biso Wilson estimate: 13.92 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.19 / Net I/σ(I): 11.16
Reflection shellResolution: 1.57→1.61 Å / Redundancy: 12.5 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1701 / CC1/2: 0.69 / Rrim(I) all: 1.16 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IT5

3it5


Resolution: 1.57→42.23 Å / SU ML: 0.1869 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 19.4403
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2029 1180 5 %
Rwork0.1513 22443 -
obs0.1538 23623 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.55 Å2
Refinement stepCycle: LAST / Resolution: 1.57→42.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1355 0 17 149 1521
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00621418
X-RAY DIFFRACTIONf_angle_d0.8711928
X-RAY DIFFRACTIONf_chiral_restr0.0496188
X-RAY DIFFRACTIONf_plane_restr0.0082255
X-RAY DIFFRACTIONf_dihedral_angle_d14.1824203
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.640.28521470.22032761X-RAY DIFFRACTION99.93
1.64-1.730.24241570.19772734X-RAY DIFFRACTION99.86
1.73-1.840.28551570.19832752X-RAY DIFFRACTION99.97
1.84-1.980.22861280.15332783X-RAY DIFFRACTION99.9
1.98-2.180.18091490.13282778X-RAY DIFFRACTION100
2.18-2.490.19641310.13722828X-RAY DIFFRACTION100
2.49-3.140.20281470.15782846X-RAY DIFFRACTION99.97
3.14-42.230.1681640.13172961X-RAY DIFFRACTION99.97

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