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- PDB-1xjt: Crystal structure of active form of P1 phage endolysin Lyz -

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Basic information

Entry
Database: PDB / ID: 1xjt
TitleCrystal structure of active form of P1 phage endolysin Lyz
ComponentsLysozyme
KeywordsHYDROLASE / open 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 / Lysozyme domain superfamily / Phage lysozyme / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CITRIC ACID / SAR-endolysin
Similarity search - Component
Biological speciesEnterobacteria phage P1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 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: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8723
Polymers21,4871
Non-polymers3842
Water2,684149
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.871, 66.871, 166.796
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-376-

HOH

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Components

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


Mass: 21487.357 Da / Num. of mol.: 1
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) / Strain (production host): Bl21(DE3)slyD-, B834(DE3) / References: UniProt: Q37875, lysozyme
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.9 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion / pH: 4.5
Details: PEG400, Sodium citrate, pH 4.5, VAPOR DIFFUSION, temperature 291.15K

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.979316, 0.97945, 0.953
SYNCHROTRONAPS 14-BM-C20.9
Detector
TypeIDDetector
CUSTOM-MADE1CCD
ADSC QUANTUM 42CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9793161
20.979451
30.9531
40.91
ReflectionResolution: 1.75→50 Å / Num. obs: 22274 / % possible obs: 96.1 % / Redundancy: 17.4 % / Rmerge(I) obs: 0.064 / Χ2: 1.026
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.75-1.8110.50.40620530.55291
1.81-1.8914.50.34620950.61294.1
1.89-1.9716.40.25621520.6994.8
1.97-2.0717.20.221750.78896.1
2.07-2.2180.1422010.85396.7
2.2-2.3818.90.10522230.87597
2.38-2.6119.30.08122530.93797.9
2.61-2.9919.70.06322941.07398.2
2.99-3.7719.70.05323381.47998.4
3.77-5018.60.05124901.81696.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT1.501data extraction
Adxvdata processing
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.75→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.985 / SU ML: 0.088 / SU R Cruickshank DPI: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.116 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1149 5.2 %RANDOM
Rwork0.208 ---
all0.209 22274 --
obs0.209 22274 96.44 %-
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: 38.337 Å2
Baniso -1Baniso -2Baniso -3
1--1.41 Å2-0.71 Å20 Å2
2---1.41 Å20 Å2
3---2.12 Å2
Refinement stepCycle: LAST / Resolution: 1.75→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1365 0 26 149 1540
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONr_bond_refined_d0.01314160.022
X-RAY DIFFRACTIONr_bond_other_d0.00112650.02
X-RAY DIFFRACTIONr_angle_refined_deg1.48519141.94
X-RAY DIFFRACTIONr_angle_other_deg0.79729363
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7891775
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.2336523.692
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.00624015
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0511315
X-RAY DIFFRACTIONr_chiral_restr0.1012020.2
X-RAY DIFFRACTIONr_gen_planes_refined0.00515980.02
X-RAY DIFFRACTIONr_gen_planes_other02830.02
X-RAY DIFFRACTIONr_nbd_refined0.2413490.3
X-RAY DIFFRACTIONr_nbd_other0.21813730.3
X-RAY DIFFRACTIONr_nbtor_other0.0917890.5
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1881690.5
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.05620.5
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.121100.3
X-RAY DIFFRACTIONr_symmetry_vdw_other0.272320.3
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.303170.5
X-RAY DIFFRACTIONr_symmetry_hbond_other0.17910.5
X-RAY DIFFRACTIONr_mcbond_it0.78710361.5
X-RAY DIFFRACTIONr_mcbond_other0.1793711.5
X-RAY DIFFRACTIONr_mcangle_it1.01313992
X-RAY DIFFRACTIONr_scbond_it1.9415963
X-RAY DIFFRACTIONr_scangle_it2.6945154.5
LS refinement shellResolution: 1.75→1.796 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.297 86
Rwork0.239 1393
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
17.5373-0.62080.05623.7753-1.3513.2705-0.17580.5061.91340.34670.2540.3842-0.8713-0.4398-0.07820.04830.0236-0.0537-0.03620.25310.2761-23.17338.0065.158
28.29752.7917-1.21353.3408-0.86112.2666-0.0747-0.35080.39920.3886-0.0472-0.026-0.19130.20760.1219-0.1181-0.0213-0.0673-0.1950.0774-0.242-10.89825.30614.001
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
119 - 979 - 97
2298 - 18698 - 186

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