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- PDB-4arj: Crystal structure of a pesticin (translocation and receptor bindi... -

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Basic information

Entry
Database: PDB / ID: 4arj
TitleCrystal structure of a pesticin (translocation and receptor binding domain) from Y. pestis and T4-lysozyme chimera
ComponentsPESTICIN, LYSOZYME
KeywordsHYDROLASE
Function / homology
Function and homology information


metabolic process / viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / host cell cytoplasm / defense response to bacterium
Similarity search - Function
Pesticin, C-terminal / Pesticin, translocation and receptor binding domain / Bacterial toxin homologue of phage lysozyme, C-term / Pesticin, receptor binding domain / Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme ...Pesticin, C-terminal / Pesticin, translocation and receptor binding domain / Bacterial toxin homologue of phage lysozyme, C-term / Pesticin, receptor binding domain / Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Endolysin / Pesticin
Similarity search - Component
Biological speciesYERSINIA PESTIS (bacteria)
ENTEROBACTERIA PHAGE T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.593 Å
AuthorsZeth, K. / Patzer, S.I. / Albrecht, R. / Braun, V.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structure and Mechanistic Studies of Pesticin, a Bacterial Homolog of Phage Lysozymes.
Authors: Patzer, S.I. / Albrecht, R. / Braun, V. / Zeth, K.
History
DepositionApr 24, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 9, 2012Provider: repository / Type: Initial release
Revision 1.1May 30, 2012Group: Other
Revision 1.2Jul 18, 2012Group: Other
Revision 1.3Oct 31, 2012Group: Structure summary
Revision 1.4Sep 25, 2013Group: Derived calculations
Revision 1.5Mar 15, 2017Group: Source and taxonomy
Revision 1.6May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: PESTICIN, LYSOZYME
B: PESTICIN, LYSOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,6167
Polymers77,1352
Non-polymers4805
Water1,40578
1
A: PESTICIN, LYSOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7603
Polymers38,5681
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PESTICIN, LYSOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8564
Polymers38,5681
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)194.874, 51.507, 107.921
Angle α, β, γ (deg.)90.00, 91.01, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PESTICIN, LYSOZYME / ENDOLYSIN / LYSIS PROTEIN / MURAMIDASE


Mass: 38567.703 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN OF PESTICIN, RESIDUES 1-167 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: CHIMERA OF THE N-TERMINAL DOMAIN OF PESTICIN FROM Y. PESTIS AND T4 LYSOZYME
Source: (gene. exp.) YERSINIA PESTIS (bacteria), (gene. exp.) ENTEROBACTERIA PHAGE T4 (virus)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q57159, UniProt: P00720, lysozyme
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 3.51 Å3/Da / Density % sol: 64.96 % / Description: NONE
Crystal growpH: 7 / Details: 20% PEG 3350 0.15 M K2(SO4), pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→73 Å / Num. obs: 33200 / % possible obs: 95.2 % / Observed criterion σ(I): 1.8 / Redundancy: 2.1 % / Biso Wilson estimate: 42.12 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.8
Reflection shellResolution: 2.6→2.66 Å / Redundancy: 2 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.8 / % possible all: 91.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MIR
Starting model: NONE

Resolution: 2.593→72.955 Å / SU ML: 0.38 / σ(F): 1.99 / Phase error: 23.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2367 1660 5 %
Rwork0.1917 --
obs0.194 33200 98.36 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.357 Å2 / ksol: 0.341 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.4196 Å20 Å21.5604 Å2
2---1.49 Å20 Å2
3----2.9296 Å2
Refinement stepCycle: LAST / Resolution: 2.593→72.955 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5083 0 25 78 5186
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0185411
X-RAY DIFFRACTIONf_angle_d1.4837011
X-RAY DIFFRACTIONf_dihedral_angle_d15.9111967
X-RAY DIFFRACTIONf_chiral_restr0.11788
X-RAY DIFFRACTIONf_plane_restr0.006900
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5929-2.66920.30431250.26172367X-RAY DIFFRACTION90
2.6692-2.75530.32331380.25672621X-RAY DIFFRACTION100
2.7553-2.85380.30841400.24272663X-RAY DIFFRACTION100
2.8538-2.96810.30081380.23542623X-RAY DIFFRACTION100
2.9681-3.10320.27591390.2142650X-RAY DIFFRACTION100
3.1032-3.26680.30011400.21622647X-RAY DIFFRACTION100
3.2668-3.47140.25441400.19612674X-RAY DIFFRACTION100
3.4714-3.73950.19971390.1832644X-RAY DIFFRACTION99
3.7395-4.11570.19871380.16272612X-RAY DIFFRACTION99
4.1157-4.71120.17591390.14392644X-RAY DIFFRACTION98
4.7112-5.93520.20531400.17632652X-RAY DIFFRACTION98
5.9352-72.98350.24471440.19152743X-RAY DIFFRACTION98
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1089-0.06180.00750.0592-0.04820.0710.0506-0.0244-0.080.04770.0143-0.06490.07780.2096-0.07220.3129-0.0545-0.21690.66480.02020.648884.517945.39818.3649
20.23740.0698-0.0180.16210.03180.0555-0.0036-0.0342-0.11090.1326-0.0091-0.01090.0480.0045-0.00640.08620.00180.00520.03550.0070.050454.711646.04717.5322
30.11140.00080.05460.12970.00770.09070.05610.0088-0.01190.0152-0.02530.04160.0403-0.05880.05080.2652-0.027-0.21080.6913-0.00640.58948.335216.347737.1073
40.0628-0.0327-0.01780.09590.01350.00690.0420.00080.0248-0.0192-0.03040.025-0.0005-0.02880.11340.16960.0773-0.15980.56330.01650.532813.098124.7242.7982
50.196-0.16440.18240.2441-0.10530.19680.12290.0530.0039-0.2202-0.0337-0.04810.09130.0370.00250.2122-0.0272-0.02550.05320.00110.123639.329225.444340.8298
60.09770.0914-0.00040.18760.02430.0078-0.06470.0345-0.0274-0.11910.05050.0285-0.04210.0086-0.0450.0753-0.03230.0501-0.03490.0737-0.061540.758921.030750.4006
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 13:152)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 153:334)
3X-RAY DIFFRACTION3CHAIN B AND (RESSEQ 12:85)
4X-RAY DIFFRACTION4CHAIN B AND (RESSEQ 86:152)
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 153:205)
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 206:334)

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