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- PDB-7q4s: Structure of the Pseudomonas aeruginosa bacteriophage JG004 endol... -

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Basic information

Entry
Database: PDB / ID: 7q4s
TitleStructure of the Pseudomonas aeruginosa bacteriophage JG004 endolysin Pae87, apo form.
ComponentsEndolysin
KeywordsHYDROLASE / endolysin / phage lysozyme / muramidase / monomodular / antimicrobial.
Function / homologyN-acetylmuramidase / N-acetylmuramidase / Lysozyme-like domain superfamily / Endolysin
Function and homology information
Biological speciesPseudomonas phage JG004 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSeoane-Blanco, M. / van Raaij, M.J.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)BFU2017-82207-P Spain
Citation
Journal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Monomodular Pseudomonas aeruginosa phage JG004 lysozyme (Pae87) contains a bacterial surface-active antimicrobial peptide-like region and a possible substrate-binding subdomain.
Authors: Vazquez, R. / Seoane-Blanco, M. / Rivero-Buceta, V. / Ruiz, S. / van Raaij, M.J. / Garcia, P.
#1: Journal: Front Microbiol / Year: 2021
Title: Mining of Gram-Negative Surface-Active Enzybiotic Candidates by Sequence-Based Calculation of Physicochemical Properties.
Authors: Vazquez, R. / Blanco-Ganan, S. / Ruiz, S. / Garcia, P.
History
DepositionNov 2, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2022Group: Database references / Derived calculations / Structure summary
Category: atom_type / citation / pdbx_contact_author
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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.year
Revision 1.2Jan 31, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
AAA: Endolysin
BBB: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7775
Polymers46,1682
Non-polymers6093
Water1,78399
1
AAA: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4863
Polymers23,0841
Non-polymers4022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2912
Polymers23,0841
Non-polymers2071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.247, 68.085, 93.100
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Endolysin


Mass: 23084.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas phage JG004 (virus) / Gene: PJG4_087 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F4YDQ3
#2: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H17NO3S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.04 Å3/Da / Density % sol: 39.6 % / Description: rounded wedge-shaped plate
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 20% (w/v) PEG 8000, 0.1 M CHES-NaOH, 20 mM Tris-HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.5→59.25 Å / Num. obs: 13640 / % possible obs: 99.7 % / Redundancy: 5.7 % / Biso Wilson estimate: 31.796 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.183 / Rpim(I) all: 0.083 / Rrim(I) all: 0.202 / Net I/σ(I): 6
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.99 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1509 / CC1/2: 0.86 / Rpim(I) all: 0.444 / Rrim(I) all: 1.087 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALS2.2.10data reduction
Aimless0.7.7data scaling
MOLREP11.7.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NM7

5nm7


Resolution: 2.5→55.018 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.904 / SU B: 14.596 / SU ML: 0.31 / Cross valid method: FREE R-VALUE / ESU R: 1.361 / ESU R Free: 0.346
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2779 658 4.839 %
Rwork0.2222 12941 -
all0.225 --
obs-13599 99.743 %
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: 56.402 Å2
Baniso -1Baniso -2Baniso -3
1--3.567 Å20 Å20 Å2
2---2.533 Å20 Å2
3---6.1 Å2
Refinement stepCycle: LAST / Resolution: 2.5→55.018 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2964 0 39 99 3102
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0133073
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162907
X-RAY DIFFRACTIONr_angle_refined_deg1.1211.6334130
X-RAY DIFFRACTIONr_angle_other_deg1.0371.5916697
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8135372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.68423.106161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.73415528
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0271514
X-RAY DIFFRACTIONr_chiral_restr0.0330.2364
X-RAY DIFFRACTIONr_chiral_restr_other0.0280.22
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023480
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02740
X-RAY DIFFRACTIONr_nbd_refined0.1580.2620
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1470.22541
X-RAY DIFFRACTIONr_nbtor_refined0.1520.21455
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.21320
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2106
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1130.27
X-RAY DIFFRACTIONr_nbd_other0.1120.244
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.150.28
X-RAY DIFFRACTIONr_mcbond_it1.1295.9751494
X-RAY DIFFRACTIONr_mcbond_other1.1275.9721493
X-RAY DIFFRACTIONr_mcangle_it2.0118.9521864
X-RAY DIFFRACTIONr_mcangle_other2.0118.9551865
X-RAY DIFFRACTIONr_scbond_it0.8256.0991579
X-RAY DIFFRACTIONr_scbond_other0.8256.1021580
X-RAY DIFFRACTIONr_scangle_it1.5339.0972266
X-RAY DIFFRACTIONr_scangle_other1.5339.1012267
X-RAY DIFFRACTIONr_lrange_it4.21468.8583439
X-RAY DIFFRACTIONr_lrange_other4.21468.8813440
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.5610.321480.31932X-RAY DIFFRACTION98.5915
2.561-2.6310.364480.293910X-RAY DIFFRACTION99.8957
2.631-2.7070.318490.297892X-RAY DIFFRACTION100
2.707-2.7910.325490.304855X-RAY DIFFRACTION99.7793
2.791-2.8820.376340.26842X-RAY DIFFRACTION99.5455
2.882-2.9830.276370.252823X-RAY DIFFRACTION99.6524
2.983-3.0960.374400.239794X-RAY DIFFRACTION99.6416
3.096-3.2220.344390.245752X-RAY DIFFRACTION100
3.222-3.3650.285440.232721X-RAY DIFFRACTION100
3.365-3.5290.241340.238697X-RAY DIFFRACTION99.7271
3.529-3.7190.283320.222683X-RAY DIFFRACTION99.8603
3.719-3.9450.269340.205627X-RAY DIFFRACTION99.8489
3.945-4.2170.246320.198595X-RAY DIFFRACTION100
4.217-4.5540.226230.182567X-RAY DIFFRACTION99.6622
4.554-4.9870.309250.186520X-RAY DIFFRACTION100
4.987-5.5740.232260.188468X-RAY DIFFRACTION100
5.574-6.4320.378230.215425X-RAY DIFFRACTION99.7773
6.432-7.8680.216170.21363X-RAY DIFFRACTION100
7.868-11.0880.152170.152292X-RAY DIFFRACTION99.6774
11.088-55.0180.26570.211183X-RAY DIFFRACTION100

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