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- PDB-3dmx: Benzene binding in the hydrophobic cavity of T4 lysozyme L99A mutant -

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Basic information

Entry
Database: PDB / ID: 3dmx
TitleBenzene binding in the hydrophobic cavity of T4 lysozyme L99A mutant
ComponentsLysozyme
KeywordsHYDROLASE / T4 lysozyme / halogen bond / hydrophobic cavity / halogenated benzene / Antimicrobial / Bacteriolytic enzyme / Glycosidase
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
BENZENE / 2-HYDROXYETHYL DISULFIDE / PHOSPHATE ION / Endolysin
Similarity search - Component
Biological speciesBacteriophage T4 (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLiu, L. / Matthews, B.W.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Halogenated benzenes bound within a non-polar cavity in T4 lysozyme provide examples of I...S and I...Se halogen-bonding
Authors: Liu, L. / Baase, W.A. / Matthews, B.W.
History
DepositionJul 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Source and taxonomy
Category: database_2 / entity_src_gen ...database_2 / entity_src_gen / 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 / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 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)19,1987
Polymers18,5861
Non-polymers6126
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.003, 60.003, 95.732
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 Lysozyme / Lysis protein / Muramidase / Endolysin


Mass: 18586.283 Da / Num. of mol.: 1 / Mutation: C54T, C97A, L99A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteriophage T4 (virus) / Gene: E / Production host: Escherichia coli (E. coli) / References: UniProt: P00720, lysozyme

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Non-polymers , 5 types, 254 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-HED / 2-HYDROXYETHYL DISULFIDE


Mass: 154.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2S2
#5: Chemical ChemComp-BNZ / BENZENE


Mass: 78.112 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.68 Å3/Da / Density % sol: 54.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 2.0-2.2 M K/Na phosphate, pH 6.9, 5mM BME and 5mM oxidized BME. Complexes were prepared by soaking or vapor diffusion methods, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.542 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 25, 2005
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.8→53 Å / Num. obs: 18791 / % possible obs: 98.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.8→1.86 Å / % possible all: 95.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3DMV

3dmv


Resolution: 1.8→45.69 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.444 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20812 956 5.1 %RANDOM
Rwork0.18176 ---
obs0.18313 17650 98.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.749 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20.07 Å20 Å2
2--0.14 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.8→45.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1335 0 27 254 1616
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221388
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9741.971870
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6795173
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.80123.58267
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.4615256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.4141514
X-RAY DIFFRACTIONr_chiral_restr0.0620.2204
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021035
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1920.2700
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2940.2957
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.2216
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.252
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.130.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.521.5859
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.82421331
X-RAY DIFFRACTIONr_scbond_it1.3763607
X-RAY DIFFRACTIONr_scangle_it2.1644.5534
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 70 -
Rwork0.304 1102 -
obs--95.67 %

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