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- PDB-5nm7: Crystal structure of Burkholderia AP3 phage endolysin -

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Basic information

Entry
Database: PDB / ID: 5nm7
TitleCrystal structure of Burkholderia AP3 phage endolysin
ComponentsPeptidoglycan-binding domain 1
KeywordsHYDROLASE / peptidoglycan binding domain / lysozyme family
Function / homology
Function and homology information


N-acetylmuramidase / N-acetylmuramidase / Muramoyl-pentapeptide Carboxypeptidase; domain 1 / PGBD-like superfamily/PGBD / PGBD superfamily / Peptidoglycan binding-like / Putative peptidoglycan binding domain / PGBD-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
GLYCINE / TRIETHYLENE GLYCOL / Endolysin
Similarity search - Component
Biological speciesBurkholderia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.72 Å
AuthorsZrubek, K. / Wisniewska, M. / Rembacz, K. / Maciejewska, B. / Drulis-Kawa, Z. / Dubin, G.
CitationJournal: Sci Rep / Year: 2017
Title: Modular endolysin of Burkholderia AP3 phage has the largest lysozyme-like catalytic subunit discovered to date and no catalytic aspartate residue.
Authors: Maciejewska, B. / Zrubek, K. / Espaillat, A. / Wisniewska, M. / Rembacz, K.P. / Cava, F. / Dubin, G. / Drulis-Kawa, Z.
History
DepositionApr 5, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 2.0May 8, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: Peptidoglycan-binding domain 1
A: Peptidoglycan-binding domain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5028
Polymers57,9762
Non-polymers5266
Water3,243180
1
G: Peptidoglycan-binding domain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3635
Polymers28,9881
Non-polymers3754
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Peptidoglycan-binding domain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1383
Polymers28,9881
Non-polymers1502
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)154.615, 154.615, 125.823
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11G-480-

HOH

21G-498-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11G
21A

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 3 - 263 / Label seq-ID: 3 - 263

Dom-IDAuth asym-IDLabel asym-ID
1GA
2AB

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Components

#1: Protein Peptidoglycan-binding domain 1 / AP3 endolysin


Mass: 28987.996 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia (bacteria) / Gene: MYA_3986 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1S5NV50*PLUS
#2: Chemical
ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H5NO2
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.5 Å3/Da / Density % sol: 50.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M SPG pH 7.0, 25% PEG 1500

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.72→26.72 Å / Num. obs: 61070 / % possible obs: 100 % / Redundancy: 9.1 % / CC1/2: 0.993 / Rmerge(I) obs: 0.126 / Net I/σ(I): 11.1
Reflection shellResolution: 1.72→1.75 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.684 / Mean I/σ(I) obs: 3.3 / CC1/2: 0.791 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.72→26.72 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.44 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.111 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23528 3029 5 %RANDOM
Rwork0.20837 ---
obs0.2097 58039 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.162 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20.08 Å20 Å2
2--0.17 Å20 Å2
3----0.55 Å2
Refinement stepCycle: 1 / Resolution: 1.72→26.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3970 0 35 180 4185
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194100
X-RAY DIFFRACTIONr_bond_other_d0.0060.023937
X-RAY DIFFRACTIONr_angle_refined_deg1.4031.9545534
X-RAY DIFFRACTIONr_angle_other_deg1.2933.0028964
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1255519
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.54422.287188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.90215646
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6791542
X-RAY DIFFRACTIONr_chiral_restr0.0830.2595
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024739
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021007
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_it1.8982.7262097
X-RAY DIFFRACTIONr_mcbond_other1.8882.7222081
X-RAY DIFFRACTIONr_mcangle_it2.784.0732609
X-RAY DIFFRACTIONr_mcangle_other2.7824.0752600
X-RAY DIFFRACTIONr_scbond_it2.6023.0312001
X-RAY DIFFRACTIONr_scbond_other2.6023.0312002
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1064.4232926
X-RAY DIFFRACTIONr_long_range_B_refined5.29422.0814849
X-RAY DIFFRACTIONr_long_range_B_other5.29422.0854850
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 29930 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1G
2A
LS refinement shellResolution: 1.72→1.765 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 227 -
Rwork0.25 4256 -
obs--100 %

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