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- PDB-3ht8: 5-chloro-2-methylphenol in complex with T4 lysozyme L99A/M102Q -

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Basic information

Entry
Database: PDB / ID: 3ht8
Title5-chloro-2-methylphenol in complex with T4 lysozyme L99A/M102Q
ComponentsLysozyme
KeywordsHYDROLASE / GLYCOSIDASE / BACTERIOLYTIC ENZYME / Antimicrobial
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
5-chloro-2-methylphenol / PHOSPHATE ION / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / REFMAC / Resolution: 1.6 Å
AuthorsBoyce, S.E. / Mobley, D.L. / Rocklin, G.J. / Graves, A.P. / Dill, K.A. / Shoichet, B.K.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site.
Authors: Boyce, S.E. / Mobley, D.L. / Rocklin, G.J. / Graves, A.P. / Dill, K.A. / Shoichet, B.K.
History
DepositionJun 11, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9794
Polymers18,6461
Non-polymers3333
Water4,414245
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.480, 60.480, 97.680
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 18646.316 Da / Num. of mol.: 1 / Mutation: S38D,L99A,M102Q,N144D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Strain: Enterobacteria Phage T4 Sensu Lato / Gene: E / Plasmid: M13 / Production host: Escherichia coli (E. coli) / References: UniProt: P00720, lysozyme
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-JZ2 / 5-chloro-2-methylphenol


Mass: 142.583 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H7ClO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.77 Å3/Da / Density % sol: 55.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2.2M sodium-potassium phosphate, 0.05M beta-mercaptoethanol, 0.05M 2-hydroxyethyldisulfide, pH 6.5, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 296 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11589 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11589 Å / Relative weight: 1
ReflectionResolution: 1.46→50 Å / Num. all: 34328 / Num. obs: 34328 / % possible obs: 92.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rmerge(I) obs: 0.071 / Χ2: 2.635 / Net I/σ(I): 37.605
Reflection shellResolution: 1.46→1.51 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.716 / Mean I/σ(I) obs: 2.46 / Num. unique all: 1663 / Χ2: 0.94 / % possible all: 45.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: REFMAC
Starting model: PDB entry 1LGU

1lgu


Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.954 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.598 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.214 1414 5.1 %RANDOM
Rwork0.188 ---
all0.19 27904 --
obs0.19 27904 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 52.57 Å2 / Biso mean: 21.809 Å2 / Biso min: 13.49 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å20.41 Å20 Å2
2--0.82 Å20 Å2
3----1.23 Å2
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1292 0 19 245 1556
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221385
X-RAY DIFFRACTIONr_angle_refined_deg1.1931.9661876
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0185176
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.80123.18869
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.17415261
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.781516
X-RAY DIFFRACTIONr_chiral_restr0.0770.2204
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021048
X-RAY DIFFRACTIONr_nbd_refined0.2050.2661
X-RAY DIFFRACTIONr_nbtor_refined0.3070.2942
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2190
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1470.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.216
X-RAY DIFFRACTIONr_mcbond_it0.7461.5855
X-RAY DIFFRACTIONr_mcangle_it1.11821331
X-RAY DIFFRACTIONr_scbond_it1.9653614
X-RAY DIFFRACTIONr_scangle_it2.8694.5537
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 86 -
Rwork0.257 1949 -
all-2035 -
obs-1949 99.41 %

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