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- PDB-7f5i: X-ray structure of Clostridium perfringens-specific amidase endolysin -

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Basic information

Entry
Database: PDB / ID: 7f5i
TitleX-ray structure of Clostridium perfringens-specific amidase endolysin
Componentsamidase
KeywordsHYDROLASE / endolysin / amidase
Function / homology
Function and homology information


N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan catabolic process / zinc ion binding
Similarity search - Function
Peptidoglycan recognition protein family domain, metazoa/bacteria / Peptidoglycan recognition protein / Animal peptidoglycan recognition proteins homologous to Bacteriophage T3 lysozyme. / Ami_2 / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase domain / N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily
Similarity search - Domain/homology
GLUTAMIC ACID / N-acetylmuramoyl-L-alanine amidase
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsKamitori, S. / Tamai, E.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18K06087, 18K07131 Japan
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Structural and biochemical characterization of the Clostridium perfringens-specific Zn 2+ -dependent amidase endolysin, Psa, catalytic domain.
Authors: Sekiya, H. / Kamitori, S. / Nariya, H. / Matsunami, R. / Tamai, E.
History
DepositionJun 22, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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: amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3505
Polymers18,9671
Non-polymers3834
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area70 Å2
ΔGint-25 kcal/mol
Surface area8040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.010, 52.870, 58.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein amidase


Mass: 18967.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (strain 13 / Type A) (bacteria)
Strain: 13 / Type A / Gene: CPE1138 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8XLA4
#2: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
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: 2.08 Å3/Da / Density % sol: 40.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 200 mM potassium bromide, 200 mM potassium thiocyanate, 0.1 M sodium acetate, 3 % w/v poly-gamma-glutamic acid, 5% w/v PEG 3350, pH 5.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jun 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→18.36 Å / Num. obs: 19657 / % possible obs: 99.7 % / Redundancy: 6.37 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 21.1
Reflection shellResolution: 1.65→1.69 Å / Rmerge(I) obs: 0.859 / Mean I/σ(I) obs: 2 / Num. unique obs: 1423

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LBA

1lba


Resolution: 1.65→18.36 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.96 / SU B: 5.437 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2047 957 4.9 %RANDOM
Rwork0.13667 ---
obs0.14009 18658 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.658 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å2-0 Å20 Å2
2--0.56 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.65→18.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1241 0 21 48 1310
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131301
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171119
X-RAY DIFFRACTIONr_angle_refined_deg1.5141.6581746
X-RAY DIFFRACTIONr_angle_other_deg1.3921.5852620
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2145152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.01724.65873
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.43215223
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.692153
X-RAY DIFFRACTIONr_chiral_restr0.0760.2152
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021474
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02264
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.0162.809617
X-RAY DIFFRACTIONr_mcbond_other5.01110.386616
X-RAY DIFFRACTIONr_mcangle_it5.8624.227766
X-RAY DIFFRACTIONr_mcangle_other5.86542.668767
X-RAY DIFFRACTIONr_scbond_it9.0623.521681
X-RAY DIFFRACTIONr_scbond_other8.872678
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.45271.933979
X-RAY DIFFRACTIONr_long_range_B_refined8.6621442
X-RAY DIFFRACTIONr_long_range_B_other8.6571439
X-RAY DIFFRACTIONr_rigid_bond_restr5.74331298
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 75 -
Rwork0.227 1339 -
obs--100 %

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