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- PDB-8yxk: X-ray structure of Clostridioides difficile endolysin Ecd09610 gl... -

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Basic information

Entry
Database: PDB / ID: 8yxk
TitleX-ray structure of Clostridioides difficile endolysin Ecd09610 glucosaminidase domain.
ComponentsPhage cell wall hydrolase
KeywordsHYDROLASE / Clostridioides difficile / endolysin
Function / homology: / Mannosyl-glycoprotein endo-beta-N-acetylglucosamidase-like domain / Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase / NlpC/P60 family / NlpC/P60 domain profile. / Endopeptidase, NLPC/P60 domain / amidase activity / Papain-like cysteine peptidase superfamily / Phage cell wall hydrolase
Function and homology information
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsKamitori, S. / Tamai, E.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)23K04944 Japan
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2024
Title: X-ray structure and mutagenesis analyses of Clostridioides difficile endolysin Ecd09610 glucosaminidase domain.
Authors: Sekiya, H. / Nonaka, Y. / Kamitori, S. / Miyaji, T. / Tamai, E.
History
DepositionApr 2, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phage cell wall hydrolase
B: Phage cell wall hydrolase


Theoretical massNumber of molelcules
Total (without water)44,7942
Polymers44,7942
Non-polymers00
Water1,44180
1
A: Phage cell wall hydrolase


Theoretical massNumber of molelcules
Total (without water)22,3971
Polymers22,3971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phage cell wall hydrolase


Theoretical massNumber of molelcules
Total (without water)22,3971
Polymers22,3971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.430, 80.470, 48.770
Angle α, β, γ (deg.)90.000, 104.117, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Phage cell wall hydrolase / Phage tail protein


Mass: 22397.062 Da / Num. of mol.: 2 / Fragment: glucosaminidase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (strain 630) (bacteria)
Gene: CD630_09610, CD630_29030 / Production host: Escherichia coli (E. coli) / References: UniProt: Q183Y3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O

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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: 2.06 Å3/Da / Density % sol: 40.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 20% (w/v) PEG 3350, 200mM sodium thiocyanate

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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 RAXIS VII / Detector: IMAGE PLATE / Date: Jul 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.87→19.322 Å / Num. obs: 29563 / % possible obs: 98.5 % / Redundancy: 3.7 % / CC1/2: 0.996 / Net I/σ(I): 9
Reflection shellResolution: 1.87→1.92 Å / Num. unique obs: 2151 / CC1/2: 0.761

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→19.322 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.886 / SU B: 4.573 / SU ML: 0.132 / Cross valid method: FREE R-VALUE / ESU R: 0.171 / ESU R Free: 0.161
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2868 1501 5.077 %
Rwork0.2472 28062 -
all0.249 --
obs-29563 98.497 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 21.628 Å2
Baniso -1Baniso -2Baniso -3
1--0.133 Å20 Å20.029 Å2
2--0.036 Å2-0 Å2
3---0.072 Å2
Refinement stepCycle: LAST / Resolution: 1.87→19.322 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2326 0 0 80 2406
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0132364
X-RAY DIFFRACTIONr_bond_other_d00.0162248
X-RAY DIFFRACTIONr_angle_refined_deg1.1861.6373166
X-RAY DIFFRACTIONr_angle_other_deg1.2451.5985192
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5495300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.54624.386114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.99815440
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.096158
X-RAY DIFFRACTIONr_chiral_restr0.0540.2302
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.022730
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02550
X-RAY DIFFRACTIONr_nbd_refined0.2052493
X-RAY DIFFRACTIONr_symmetry_nbd_other0.221856
X-RAY DIFFRACTIONr_nbtor_refined0.1630.21183
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.21072
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.283
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.148216
X-RAY DIFFRACTIONr_nbd_other0.193226
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1780.210
X-RAY DIFFRACTIONr_mcbond_it2.0612.081206
X-RAY DIFFRACTIONr_mcbond_other2.0542.0771205
X-RAY DIFFRACTIONr_mcangle_it2.9083.1081504
X-RAY DIFFRACTIONr_mcangle_other2.9093.1121505
X-RAY DIFFRACTIONr_scbond_it2.7832.4151158
X-RAY DIFFRACTIONr_scbond_other2.7832.421159
X-RAY DIFFRACTIONr_scangle_it4.2313.481662
X-RAY DIFFRACTIONr_scangle_other4.233.4841663
X-RAY DIFFRACTIONr_lrange_it5.31724.692716
X-RAY DIFFRACTIONr_lrange_other5.31424.6992709
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.9190.3921130.3652038X-RAY DIFFRACTION97.7283
1.919-1.9710.346880.3461984X-RAY DIFFRACTION97.0492
1.971-2.0280.3281050.2891950X-RAY DIFFRACTION97.532
2.028-2.090.3411030.2681900X-RAY DIFFRACTION98.7673
2.09-2.1590.308860.2461810X-RAY DIFFRACTION97.7824
2.159-2.2340.388950.2721803X-RAY DIFFRACTION97.8351
2.234-2.3180.331900.3051730X-RAY DIFFRACTION98.2191
2.318-2.4130.264760.2271684X-RAY DIFFRACTION98.9876
2.413-2.520.323910.2341567X-RAY DIFFRACTION98.6905
2.52-2.6430.273820.2281541X-RAY DIFFRACTION99.3876
2.643-2.7850.3820.2261439X-RAY DIFFRACTION98.959
2.785-2.9530.278780.241402X-RAY DIFFRACTION99.5962
2.953-3.1560.281690.2431300X-RAY DIFFRACTION99.4913
3.156-3.4080.297870.2531193X-RAY DIFFRACTION99.5334
3.408-3.7310.277510.2481144X-RAY DIFFRACTION99.2525
3.731-4.1680.264470.2141002X-RAY DIFFRACTION99.7148
4.168-4.8070.197610.18902X-RAY DIFFRACTION99.5863
4.807-5.8720.245470.227756X-RAY DIFFRACTION99.3812
5.872-8.2410.179370.227591X-RAY DIFFRACTION99.3671
8.241-19.3220.341130.207326X-RAY DIFFRACTION91.3747

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