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- PDB-5kim: PSEUDO T4 LYSOZYME MUTANT - Y88PHE-I -

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Basic information

Entry
Database: PDB / ID: 5kim
TitlePSEUDO T4 LYSOZYME MUTANT - Y88PHE-I
ComponentsEndolysin
KeywordsHYDROLASE / HALOGEN BONDS / 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
Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme-like domain superfamily
Similarity search - Domain/homology
2-HYDROXYETHYL DISULFIDE / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsScholfield, M.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1152494 United States
CitationJournal: Biochemistry / Year: 2017
Title: Structure-Energy Relationships of Halogen Bonds in Proteins.
Authors: Scholfield, M.R. / Ford, M.C. / Carlsson, A.C. / Butta, H. / Mehl, R.A. / Ho, P.S.
History
DepositionJun 16, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Database references
Revision 1.2Jun 14, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7674
Polymers19,5671
Non-polymers2003
Water6,449358
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.283, 60.283, 96.197
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-501-

HOH

21A-534-

HOH

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Components

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


Mass: 19567.143 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Plasmid: PBAD / Production host: Escherichia coli (E. coli) / References: UniProt: P00720, lysozyme
#2: Chemical ChemComp-HED / 2-HYDROXYETHYL DISULFIDE


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / 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: 2.73 Å3/Da / Density % sol: 54.88 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 2.0M KPO4, 50mM 2-HYDROXYETHYLDISULFID, 50mM 2-MERCAPTOETHANOL, PH6.9
PH range: 6.6-7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Apr 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 33148 / % possible obs: 99.9 % / Redundancy: 13 % / Biso Wilson estimate: 13.06 Å2 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.014 / Rrim(I) all: 0.06 / Χ2: 3.156 / Net I/av σ(I): 70.423 / Net I/σ(I): 23.4 / Num. measured all: 431722
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.5-1.535.90.341199.1
1.53-1.558.80.3171100
1.55-1.589.30.2461100
1.58-1.629.60.2231100
1.62-1.659.80.1961100
1.65-1.69100.1841100
1.69-1.7310.20.1721100
1.73-1.7810.80.151100
1.78-1.8311.20.1311100
1.83-1.8911.20.1211100
1.89-1.9610.90.1371100
1.96-2.0412.80.091100
2.04-2.1312.40.0921100
2.13-2.2414.20.0711100
2.24-2.38150.0681100
2.38-2.5616.80.061100
2.56-2.8217.60.0581100
2.82-3.2319.90.051100
3.23-4.0720.90.0451100
4.07-5021.60.043199.4

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L63

1l63


Resolution: 1.5→35.374 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.78
RfactorNum. reflection% reflection
Rfree0.1844 3787 6.06 %
Rwork0.1604 --
obs0.1619 62441 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 54.02 Å2 / Biso mean: 16.8073 Å2 / Biso min: 2.89 Å2
Refinement stepCycle: final / Resolution: 1.5→35.374 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1292 0 10 358 1660
Biso mean--16.41 29.4 -
Num. residues----162
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051489
X-RAY DIFFRACTIONf_angle_d0.8172033
X-RAY DIFFRACTIONf_chiral_restr0.071221
X-RAY DIFFRACTIONf_plane_restr0.005267
X-RAY DIFFRACTIONf_dihedral_angle_d18.581629
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4985-1.51750.27171270.23811904203188
1.5175-1.53750.21881420.20392181232399
1.5375-1.55850.22251420.187822012343100
1.5585-1.58080.25851460.17722102356100
1.5808-1.60440.18641380.166921222260100
1.6044-1.62950.17161380.166322452383100
1.6295-1.65620.17761400.176721492289100
1.6562-1.68470.20891340.176722032337100
1.6847-1.71540.20791520.183821612313100
1.7154-1.74840.23421460.181321902336100
1.7484-1.7840.22281400.18321722312100
1.784-1.82280.20671440.171721892333100
1.8228-1.86520.21261360.178622072343100
1.8652-1.91190.19621350.18182132226799
1.9119-1.96360.2031410.16992199234099
1.9636-2.02130.18721440.164921712315100
2.0213-2.08660.21500.17222200235099
2.0866-2.16110.19031290.164921342263100
2.1611-2.24770.16921460.150321792325100
2.2477-2.34990.15781420.153821972339100
2.3499-2.47380.18971360.157422022338100
2.4738-2.62870.19721460.161421852331100
2.6287-2.83160.17561400.158921722312100
2.8316-3.11640.23791310.154821912322100
3.1164-3.5670.14431360.140522022338100
3.567-4.49260.14031400.125221642304100
4.4926-35.38390.1661460.165621922338100

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