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- PDB-5i14: Truncated and mutated T4 lysozyme -

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Basic information

Entry
Database: PDB / ID: 5i14
TitleTruncated and mutated T4 lysozyme
Componentsmutated and truncated T4 lysozyme
KeywordsHYDROLASE / T4 lysozyme
Function / homology
Function and homology information


viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / host cell cytoplasm / defense response to bacterium
Similarity search - Function
Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
NICKEL (II) ION / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.745 Å
AuthorsKlima, M. / Boura, E.
CitationJournal: Protein Sci. / Year: 2017
Title: Metal ions-binding T4 lysozyme as an intramolecular protein purification tag compatible with X-ray crystallography.
Authors: Boura, E. / Baumlova, A. / Chalupska, D. / Dubankova, A. / Klima, M.
History
DepositionFeb 5, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Structure summary / Category: citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _struct.title
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: mutated and truncated T4 lysozyme
B: mutated and truncated T4 lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5526
Polymers27,3172
Non-polymers2354
Water3,549197
1
A: mutated and truncated T4 lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8354
Polymers13,6581
Non-polymers1763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: mutated and truncated T4 lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7172
Polymers13,6581
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.088, 61.206, 69.806
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein mutated and truncated T4 lysozyme


Mass: 13658.495 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: P00720*PLUS
#2: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.37 Å3/Da / Density % sol: 48.08 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 6000, 100mM MES pH 5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9796 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.745→46.021 Å / Num. obs: 26668 / % possible obs: 99.45 % / Redundancy: 7.1 % / CC1/2: 1 / Rmerge(I) obs: 0.04921 / Net I/σ(I): 22.46
Reflection shellResolution: 1.745→1.808 Å / Rmerge(I) obs: 1.322 / Mean I/σ(I) obs: 1.33

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GBR (N terminal T4L only)

4gbr


Resolution: 1.745→46.021 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.62
RfactorNum. reflection% reflection
Rfree0.2455 1118 4.19 %
Rwork0.2128 --
obs0.2142 26663 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.745→46.021 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1868 0 4 197 2069
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061910
X-RAY DIFFRACTIONf_angle_d0.9422583
X-RAY DIFFRACTIONf_dihedral_angle_d12.3673
X-RAY DIFFRACTIONf_chiral_restr0.04277
X-RAY DIFFRACTIONf_plane_restr0.004336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7453-1.82470.34071330.33533036X-RAY DIFFRACTION96
1.8247-1.92090.3341370.30653144X-RAY DIFFRACTION100
1.9209-2.04120.31931390.2663175X-RAY DIFFRACTION100
2.0412-2.19880.2861390.23033168X-RAY DIFFRACTION100
2.1988-2.42010.26991390.22623184X-RAY DIFFRACTION100
2.4201-2.77030.29781410.22093219X-RAY DIFFRACTION100
2.7703-3.49010.23861410.21423231X-RAY DIFFRACTION100
3.4901-46.03710.20061490.18273388X-RAY DIFFRACTION100

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