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- PDB-5vnr: X-ray structure of perdeuterated T4 lysozyme cysteine-free pseudo... -

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Basic information

Entry
Database: PDB / ID: 5vnr
TitleX-ray structure of perdeuterated T4 lysozyme cysteine-free pseudo-wild type at cryogenic temperature
ComponentsEndolysinLysin
KeywordsHYDROLASE / T4 lysozyme / Neutron Crystallography / Hydrogen bonding network / Hydrogen bond / Water
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
Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Lysozyme-like domain superfamily
Similarity search - Domain/homology
2-HYDROXYETHYL DISULFIDE / PHOSPHATE ION / Endolysin / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.631 Å
AuthorsLi, L. / Shukla, S. / Meilleur, F. / Standaert, R.F. / Pierce, J. / Myles, D.A.A. / Cuneo, M.J.
CitationJournal: Protein Sci. / Year: 2017
Title: Neutron crystallographic studies of T4 lysozyme at cryogenic temperature.
Authors: Li, L. / Shukla, S. / Meilleur, F. / Standaert, R.F. / Pierce, J. / Myles, D.A.A. / Cuneo, M.J.
History
DepositionMay 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Sep 9, 2020Group: Derived calculations / Structure summary / Category: pdbx_struct_conn_angle / struct / struct_conn
Item: _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id ..._pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct.title / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0647
Polymers18,6281
Non-polymers4356
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.830, 59.830, 95.461
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 18628.363 Da / Num. of mol.: 1 / Mutation: C54T, C97A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: e, T4Tp126 / Production host: Escherichia coli (E. coli) / References: UniProt: D9IEF7, UniProt: P00720*PLUS, lysozyme

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Non-polymers , 6 types, 299 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-HED / 2-HYDROXYETHYL DISULFIDE


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 2.65 Å3/Da / Density % sol: 53.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: ~2.0 M Na/K phosphate, pH 6-7, 250 mM NaCl, 40mM 2-hydroxyethyl disulfide
PH range: 6-7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.63→50 Å / Num. obs: 25255 / % possible obs: 99.7 % / Redundancy: 10.1 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 20.1

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LW9

1lw9


Resolution: 1.631→28.546 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1856 2009 7.97 %
Rwork0.1583 --
obs0.1604 25217 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.631→28.546 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1308 0 22 293 1623
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061432
X-RAY DIFFRACTIONf_angle_d0.791933
X-RAY DIFFRACTIONf_dihedral_angle_d19.328555
X-RAY DIFFRACTIONf_chiral_restr0.047211
X-RAY DIFFRACTIONf_plane_restr0.005249
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6305-1.67130.21811410.17811612X-RAY DIFFRACTION99
1.6713-1.71650.18621350.14941636X-RAY DIFFRACTION100
1.7165-1.7670.19351430.15551638X-RAY DIFFRACTION100
1.767-1.8240.21741440.1561628X-RAY DIFFRACTION100
1.824-1.88920.1771440.15361638X-RAY DIFFRACTION100
1.8892-1.96480.1861390.15561615X-RAY DIFFRACTION99
1.9648-2.05420.15161490.14941668X-RAY DIFFRACTION100
2.0542-2.16250.17221410.14681637X-RAY DIFFRACTION100
2.1625-2.29790.18751400.14581648X-RAY DIFFRACTION100
2.2979-2.47520.18471440.15551672X-RAY DIFFRACTION100
2.4752-2.72420.18521430.16171670X-RAY DIFFRACTION100
2.7242-3.11790.18861430.16181669X-RAY DIFFRACTION100
3.1179-3.92660.17631490.14291686X-RAY DIFFRACTION99
3.9266-28.55050.19851540.18251791X-RAY DIFFRACTION100

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