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- PDB-1xju: Crystal structure of secreted inactive form of P1 phage endolysin Lyz -

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Basic information

Entry
Database: PDB / ID: 1xju
TitleCrystal structure of secreted inactive form of P1 phage endolysin Lyz
ComponentsLysozyme
KeywordsHYDROLASE / secreted inactive conformation
Function / homology
Function and homology information


peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to bacterium / host cell plasma membrane / membrane
Similarity search - Function
SAR-endolysin-like / : / Lysozyme - #40 / Endolysin T4 type / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesEnterobacteria phage P1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.07 Å
AuthorsArockiasamy, A. / Sacchettini, J.C.
CitationJournal: Science / Year: 2005
Title: Disulfide isomerization after membrane release of its SAR domain activates P1 lysozyme.
Authors: Xu, M. / Arulandu, A. / Struck, D.K. / Swanson, S. / Sacchettini, J.C. / Young, R.
History
DepositionSep 24, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysozyme
B: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,72610
Polymers36,9582
Non-polymers7698
Water10,269570
1
A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6713
Polymers18,4791
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0557
Polymers18,4791
Non-polymers5766
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
B: Lysozyme
hetero molecules

A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,72610
Polymers36,9582
Non-polymers7698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area3760 Å2
ΔGint-90 kcal/mol
Surface area16110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.349, 59.786, 76.228
Angle α, β, γ (deg.)90.00, 102.51, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lysozyme / Lysis protein / Muramidase / Endolysin / Protein gp17


Mass: 18478.969 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage P1 (virus) / Genus: P1-like viruses / Gene: 17, LYSA, LyZ / Production host: Escherichia coli (E. coli) / References: UniProt: Q37875, lysozyme
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 570 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.7 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion / pH: 4.5
Details: sodium acetate, PEG4000, pH 4.5, VAPOR DIFFUSION, temperature 291.15K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.07→50 Å / Num. obs: 116001 / % possible obs: 90.2 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.057
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.07-1.112.40.318151.9
1.11-1.152.80.238168.5
1.15-1.213.40.201191
1.21-1.274.90.239197.2
1.27-1.355.80.206197.6
1.35-1.457.20.172198.4
1.45-1.67.40.105198.9
1.6-1.837.30.067199.3
1.83-2.317.20.047199.8
2.31-505.30.032198.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT1.501data extraction
Adxvdata processing
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.07→46.62 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.971 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.029 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.153 5779 5 %RANDOM
Rwork0.133 ---
all0.134 ---
obs0.134 115921 90.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 9.67 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å2-0.02 Å2
2---0.09 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.07→46.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2430 0 40 570 3040
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0212512
X-RAY DIFFRACTIONr_bond_other_d0.0010.022218
X-RAY DIFFRACTIONr_angle_refined_deg1.9171.943391
X-RAY DIFFRACTIONr_angle_other_deg0.85535150
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3355307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.5723.496123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.28115433
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0111526
X-RAY DIFFRACTIONr_chiral_restr0.2830.2349
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022787
X-RAY DIFFRACTIONr_gen_planes_other00.02515
X-RAY DIFFRACTIONr_nbd_refined0.2390.3589
X-RAY DIFFRACTIONr_nbd_other0.2090.32401
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0930.51402
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.5617
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.338
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3310.3133
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2040.581
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it2.15821956
X-RAY DIFFRACTIONr_mcbond_other1.272644
X-RAY DIFFRACTIONr_mcangle_it2.37832444
X-RAY DIFFRACTIONr_scbond_it3.33421123
X-RAY DIFFRACTIONr_scangle_it3.9353947
X-RAY DIFFRACTIONr_rigid_bond_restr2.77915704
X-RAY DIFFRACTIONr_sphericity_free8.2375570
X-RAY DIFFRACTIONr_sphericity_bonded2.89954688
LS refinement shellResolution: 1.07→1.098 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.242 232
Rwork0.214 4483

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