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- PDB-6yj1: The M23 peptidase domain of the Staphylococcal phage 2638A endolysin -

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Basic information

Entry
Database: PDB / ID: 6yj1
TitleThe M23 peptidase domain of the Staphylococcal phage 2638A endolysin
ComponentsORF007
KeywordsVIRAL PROTEIN / zinc metallopeptidase / bacteriophage / endolysin / M23 peptidase
Function / homology
Function and homology information


N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan catabolic process / killing of cells of another organism / defense response to bacterium / metal ion binding
Similarity search - Function
Bacterial SH3 domain / SH3b domain profile. / Bacterial SH3 domain homologues / SH3-like domain, bacterial-type / Peptidase M23 / Peptidase family M23 / Duplicated hybrid motif / 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
Biological speciesStaphylococcus phage 2638A (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDunne, M. / Ernst, P. / Sobieraj, A. / Pluckthun, A. / Loessner, M.J.
CitationJournal: To Be Published
Title: (CASP target) Crystal structure of the M23 peptidase domain of Staphylococcal phage 2638A endolysin
Authors: Sobieraj, A. / Dunne, M. / Ernst, P. / Pluckthun, A. / Loessner, M.J.
History
DepositionApr 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ORF007
B: ORF007
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7044
Polymers42,5732
Non-polymers1312
Water2,162120
1
A: ORF007
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3522
Polymers21,2861
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ORF007
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3522
Polymers21,2861
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.890, 56.380, 110.490
Angle α, β, γ (deg.)90.000, 92.840, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'A' and (resid 6 through 172 or resid 174))A6 - 171
221(chain 'B' and (resid 6 through 172 or resid 174))B6 - 171

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Components

#1: Protein ORF007


Mass: 21286.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus phage 2638A (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: Q4ZD58
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.48 Å3/Da / Density % sol: 50.33 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: Protein buffer: 20 mM Tris, 150 mM NaCl, pH 7.4 Crystallization buffer: 0.2 M sodium chloride, 30 % (v/v) PEG 300, pH 5.7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→39.43 Å / Num. obs: 17866 / % possible obs: 95.06 % / Redundancy: 6.01 % / Biso Wilson estimate: 29.08 Å2 / CC1/2: 0.986 / CC star: 0.996 / Rmerge(I) obs: 0.1612 / Rpim(I) all: 0.0696 / Rrim(I) all: 0.1761 / Net I/σ(I): 7.59
Reflection shellResolution: 2.3→2.382 Å / Redundancy: 5.74 % / Rmerge(I) obs: 0.5327 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 1664 / CC1/2: 0.911 / CC star: 0.976 / Rpim(I) all: 0.235 / Rrim(I) all: 0.585 / % possible all: 89.46

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
PHASERphasing
PHENIX1.15.2refinement
Cootmodel building
REFMAC5.8refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LXC

4lxc


Resolution: 2.3→39.43 Å / SU ML: 0.2541 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 40.2503
RfactorNum. reflection% reflection
Rfree0.3096 888 4.99 %
Rwork0.2513 --
obs0.2543 17795 95.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 32 Å2
Refinement stepCycle: LAST / Resolution: 2.3→39.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2704 0 2 120 2826
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00842768
X-RAY DIFFRACTIONf_angle_d1.0743744
X-RAY DIFFRACTIONf_chiral_restr0.0557376
X-RAY DIFFRACTIONf_plane_restr0.0055500
X-RAY DIFFRACTIONf_dihedral_angle_d4.32521618
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.440.34561390.26632626X-RAY DIFFRACTION88.51
2.44-2.630.28431420.24842735X-RAY DIFFRACTION93.62
2.63-2.90.3231470.25042811X-RAY DIFFRACTION95.98
2.9-3.320.33171520.27472882X-RAY DIFFRACTION97.31
3.32-4.180.28451490.23272853X-RAY DIFFRACTION96.03
4.18-39.430.3131590.25263000X-RAY DIFFRACTION98.97

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