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- PDB-5kig: PSEUDO T4 LYSOZYME MUTANT - Y88F -

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Basic information

Entry
Database: PDB / ID: 5kig
TitlePSEUDO T4 LYSOZYME MUTANT - Y88F
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
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
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 / 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

Downloads & links

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Assembly

Deposited unit
A: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5952
Polymers19,4411
Non-polymers1541
Water6,035335
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.368, 60.368, 96.571
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-478-

HOH

21A-485-

HOH

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Components

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


Mass: 19441.246 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 2.76 Å3/Da / Density % sol: 55.48 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 2.0M KPO4, 50MM 2-HYDROXYETHYLDISULFIDE, 50MM 2-MERCAPTOETHANOL, PH6.9

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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 15, 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: 33527 / % possible obs: 99.3 % / Redundancy: 8.1 % / Biso Wilson estimate: 12.1 Å2 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.021 / Rrim(I) all: 0.064 / Χ2: 2.423 / Net I/av σ(I): 42.296 / Net I/σ(I): 18.2 / Num. measured all: 269948
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.5-1.533.30.399194.8
1.53-1.555.70.367199.7
1.55-1.586.50.3451100
1.58-1.626.70.2921100
1.62-1.6570.2681100
1.65-1.697.10.2481100
1.69-1.736.90.2161100
1.73-1.787.30.191100
1.78-1.837.70.174199.9
1.83-1.897.20.149199.6
1.89-1.964.90.142198.2
1.96-2.048.10.108199.9
2.04-2.137.20.096199.9
2.13-2.248.50.083199.4
2.24-2.388.20.072198.8
2.38-2.5611.20.066199.8
2.56-2.8210.70.058199.8
2.82-3.2313.20.049199.9
3.23-4.078.30.04197.5
4.07-5014.20.032199.1

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Processing

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

1l63


Resolution: 1.5→22.988 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.75
RfactorNum. reflection% reflection
Rfree0.1956 3747 5.97 %
Rwork0.1626 --
obs0.1645 62766 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 51.84 Å2 / Biso mean: 16.3394 Å2 / Biso min: 3.68 Å2
Refinement stepCycle: final / Resolution: 1.5→22.988 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1291 0 8 335 1634
Biso mean--35.63 27.97 -
Num. residues----162
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051457
X-RAY DIFFRACTIONf_angle_d0.7971987
X-RAY DIFFRACTIONf_chiral_restr0.066218
X-RAY DIFFRACTIONf_plane_restr0.005260
X-RAY DIFFRACTIONf_dihedral_angle_d19.144605
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 (%)
1.4928-1.51170.28141020.2651697179975
1.5117-1.53160.29711420.22662150229296
1.5316-1.55250.24741270.21062197232499
1.5525-1.57470.20141400.188222112351100
1.5747-1.59820.20111480.179222382386100
1.5982-1.62320.24771380.187822392377100
1.6232-1.64980.21891360.177822222358100
1.6498-1.67820.2041460.183222552401100
1.6782-1.70870.20061320.176821872319100
1.7087-1.74160.20841460.171722482394100
1.7416-1.77710.22821450.171322902435100
1.7771-1.81570.21791370.170921572294100
1.8157-1.8580.17991430.163322182361100
1.858-1.90440.20161270.17762135226296
1.9044-1.95590.20011450.18122114225996
1.9559-2.01340.16591500.157422322382100
2.0134-2.07830.19661440.163722242368100
2.0783-2.15260.17861440.151622352379100
2.1526-2.23870.19191380.15242171230998
2.2387-2.34050.19071520.15932119227197
2.3405-2.46370.19671380.157522272365100
2.4637-2.61790.22171340.162722552389100
2.6179-2.81970.21071400.16621812321100
2.8197-3.10280.25481420.17122372379100
3.1028-3.55040.14851280.14332253238199
3.5504-4.46780.1441320.12692098223096
4.4678-22.99040.18271510.158222292380100

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