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- PDB-7q47: Endolysin from bacteriophage Enc34, catalytic domain -

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Basic information

Entry
Database: PDB / ID: 7q47
TitleEndolysin from bacteriophage Enc34, catalytic domain
ComponentsEndolysin
KeywordsHYDROLASE / beta-N-acetylglucosaminidase / peptidoglycan / bacteriophage
Function / homologymembrane => GO:0016020 / Endolysin
Function and homology information
Biological speciesEnterobacter phage Enc34 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsCernooka, E. / Rumnieks, J. / Kazaks, A. / Tars, K.
Funding support Latvia, 2items
OrganizationGrant numberCountry
Other privateSIA Mikrotikls scholarship for exact and medical sciences Latvia
Other governmentESF project 8.2.2.0/20/I/006 Latvia
CitationJournal: Sci Rep / Year: 2022
Title: Diversity of the lysozyme fold: structure of the catalytic domain from an unusual endolysin encoded by phage Enc34.
Authors: Cernooka, E. / Rumnieks, J. / Zrelovs, N. / Tars, K. / Kazaks, A.
History
DepositionOct 29, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 2.0Feb 9, 2022Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / atom_type ...atom_site / atom_type / chem_comp / entity / pdbx_contact_author / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_restr_ncs / refine_ls_shell / software / struct_asym / struct_conn / struct_ncs_dom / struct_ncs_dom_lim
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_diffrn_id / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _software.classification / _software.name / _software.version / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Model completeness
Details: Several improvements have neen made compared to the original model: - missing OXT atom added to chain A; - an alternative conformation modeled for residue Met123B; - an alternative ...Details: Several improvements have neen made compared to the original model: - missing OXT atom added to chain A; - an alternative conformation modeled for residue Met123B; - an alternative conformation for Glu118 in both protein chains replaced with a chloride ion to better explain the observed electron density; - minor adjustments to side chain conformations for Arg36A, Lys84A, Arg140A; - more water molecules modeled; - NCS restraints used in refinement.
Provider: author / Type: Coordinate replacement
Revision 2.1Jun 1, 2022Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 2.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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
A: Endolysin
B: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5066
Polymers38,3892
Non-polymers1174
Water4,756264
1
A: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2302
Polymers19,1941
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2764
Polymers19,1941
Non-polymers813
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.304, 128.993, 36.279
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 4 - 168 / Label seq-ID: 5 - 169

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Endolysin


Mass: 19194.439 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter phage Enc34 (virus) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H6WYJ5
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.99 Å3/Da / Density % sol: 38.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.1 M phosphate/citrate, 0.2 M sodium chloride, 20% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.6→45.89 Å / Num. obs: 41411 / % possible obs: 100 % / Redundancy: 12.156 % / Biso Wilson estimate: 30.667 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.168 / Rrim(I) all: 0.175 / Χ2: 0.903 / Net I/σ(I): 9.9 / Num. measured all: 503383
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.6-1.711.3941.5252.0377078676667650.7681.597100
1.7-1.811.9621.0793.1564035535353530.8831.127100
1.8-1.912.4430.7684.8353593430743070.9450.801100
1.9-212.6220.5616.8644076349234920.9690.585100
2-2.212.6430.3689.9966048522452240.9850.383100
2.2-2.512.4740.24313.0463355508050790.990.253100
2.5-312.3620.15716.8857102462046190.9930.163100
3-412.0760.11620.3744767370837070.9950.121100
4-511.7080.10621.8715900135813580.9940.11100
5-45.8911.5650.08921.9417429151115070.9950.09399.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Enc34 ORF39-SeMet

Resolution: 1.6→45.89 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.052 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2091 2071 5 %RANDOM
Rwork0.1774 ---
obs0.179 39341 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.8 Å2 / Biso mean: 24.451 Å2 / Biso min: 11.81 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å2-0 Å20 Å2
2--0.78 Å2-0 Å2
3----0.99 Å2
Refinement stepCycle: final / Resolution: 1.6→45.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2591 0 4 264 2859
Biso mean--29 33.59 -
Num. residues----324
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132667
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172490
X-RAY DIFFRACTIONr_angle_refined_deg1.5191.6573623
X-RAY DIFFRACTIONr_angle_other_deg1.4221.5895714
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1045325
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.02421.696171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.75615445
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4891528
X-RAY DIFFRACTIONr_chiral_restr0.0750.2348
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023111
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02661
Refine LS restraints NCS

Ens-ID: 1 / Number: 4957 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.14 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 151 -
Rwork0.3 2866 -
all-3017 -
obs--99.97 %

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