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- PDB-4eks: T4 Lysozyme L99A/M102H with Isoxazole Bound -

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Basic information

Entry
Database: PDB / ID: 4eks
TitleT4 Lysozyme L99A/M102H with Isoxazole Bound
ComponentsLysozyme
KeywordsHYDROLASE / Alkylation of Cys97
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
1,2-benzisoxazole / ACETATE ION / BETA-MERCAPTOETHANOL / 2-HYDROXYETHYL DISULFIDE / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.64 Å
AuthorsMerski, M. / Shoichet, B.K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Engineering a model protein cavity to catalyze the Kemp elimination.
Authors: Merski, M. / Shoichet, B.K.
History
DepositionApr 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Database references
Revision 1.2Oct 17, 2012Group: Database references
Revision 1.3Sep 13, 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 / struct_conn / 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_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysozyme
B: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,17117
Polymers42,8092
Non-polymers1,36215
Water5,675315
1
A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0869
Polymers21,4041
Non-polymers6828
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0858
Polymers21,4041
Non-polymers6817
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Lysozyme
hetero molecules

B: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,17117
Polymers42,8092
Non-polymers1,36215
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,y-1/2,-z1
Buried area2120 Å2
ΔGint-12 kcal/mol
Surface area16280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.300, 75.370, 52.650
Angle α, β, γ (deg.)90.00, 93.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 21404.426 Da / Num. of mol.: 2 / Mutation: T21C/S38D/L99A/M102H/E108V/S117V/T142C/N144D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: E / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00720, lysozyme

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Non-polymers , 6 types, 330 molecules

#2: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical ChemComp-0R1 / 1,2-benzisoxazole


Mass: 119.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H5NO
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-HED / 2-HYDROXYETHYL DISULFIDE


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / 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: 2.25 Å3/Da / Density % sol: 45.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 30% (w/v) PEG-6000, 0.3 M LiSO4, 3% (w/v) TMAO, 50 mM 2-mercaptoethanol, 50 mM 2-hydroxyethyl disulfide, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.116 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 22, 2010
RadiationMonochromator: two flat Si(111) crystals, mounted in a model DCM from Khozu
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionResolution: 1.64→50 Å / Num. obs: 43970 / % possible obs: 95.2 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.052 / Net I/σ(I): 14.23
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.64-1.730.3133.04197.8
1.73-1.840.2214.32197.2
1.84-1.970.1476.39197
1.97-2.120.09210.13196.3
2.12-2.320.06514.23195.7
2.32-2.590.0518.88194.8
2.59-2.990.03823.38193.7
2.99-3.670.02930.84191.3
3.67-5.190.02239.66189.9
5.19-500.0239.98187.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
XDSdata reduction
PHENIX1.7.1_743phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4E97

4e97


Resolution: 1.64→48.227 Å / Occupancy max: 1 / Occupancy min: 0.2 / SU ML: 0.4 / σ(F): 2 / Phase error: 17.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.198 1771 4.03 %
Rwork0.1713 --
obs0.1724 43969 95.25 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.801 Å2 / ksol: 0.382 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.4679 Å20 Å20.256 Å2
2--1.2315 Å20 Å2
3----0.7636 Å2
Refinement stepCycle: LAST / Resolution: 1.64→48.227 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2760 0 79 315 3154
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012997
X-RAY DIFFRACTIONf_angle_d1.2054050
X-RAY DIFFRACTIONf_dihedral_angle_d13.1261134
X-RAY DIFFRACTIONf_chiral_restr0.078439
X-RAY DIFFRACTIONf_plane_restr0.005523
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.68440.30441420.2433301X-RAY DIFFRACTION98
1.6844-1.73390.25481380.21373328X-RAY DIFFRACTION98
1.7339-1.78990.22791380.20353307X-RAY DIFFRACTION97
1.7899-1.85390.22631400.18593282X-RAY DIFFRACTION97
1.8539-1.92810.19851390.17193312X-RAY DIFFRACTION97
1.9281-2.01580.21561350.1653273X-RAY DIFFRACTION97
2.0158-2.12210.19961370.16033265X-RAY DIFFRACTION96
2.1221-2.25510.19781350.15823241X-RAY DIFFRACTION96
2.2551-2.42920.20671430.16033258X-RAY DIFFRACTION95
2.4292-2.67360.20091300.16893235X-RAY DIFFRACTION95
2.6736-3.06050.19051310.17513188X-RAY DIFFRACTION93
3.0605-3.85560.17451330.15823109X-RAY DIFFRACTION91
3.8556-48.2480.16231300.16493099X-RAY DIFFRACTION89
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.77130.1890.26220.4636-0.40230.61990.1322-0.36380.37710.28310.05540.2053-0.2806-0.15020.4011-0.23360.09960.1322-0.1906-0.1152-0.27846.479113.691510.2451
20.48170.23830.05720.56820.27730.52520.0010.0307-0.043-0.00890.042-0.02270.07140.0032-0.00950.0401-0.0068-0.01090.03830.00550.044830.549220.3242-9.0777
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and (resid -10:164 or resid 201:208)A-10 - 164
2X-RAY DIFFRACTION1chain A and (resid -10:164 or resid 201:208)A201 - 208
3X-RAY DIFFRACTION2chain B and (resid -9:164 or resid 201:207)B-9 - 164
4X-RAY DIFFRACTION2chain B and (resid -9:164 or resid 201:207)B201 - 207

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