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- PDB-4i7m: T4 Lysozyme L99A/M102H with 2-allylphenol bound -

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Basic information

Entry
Database: PDB / ID: 4i7m
TitleT4 Lysozyme L99A/M102H with 2-allylphenol bound
ComponentsLysozyme
KeywordsHYDROLASE
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-ALLYLPHENOL / ACETATE ION / BETA-MERCAPTOETHANOL / 2-HYDROXYETHYL DISULFIDE / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsMerski, M. / Shoichet, B.K.
CitationJournal: J.Med.Chem. / Year: 2013
Title: The impact of introducing a histidine into an apolar cavity site on docking and ligand recognition.
Authors: Merski, M. / Shoichet, B.K.
History
DepositionNov 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 20, 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_auth_seq_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

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Assembly

Deposited unit
A: Lysozyme
B: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,23817
Polymers42,8092
Non-polymers1,43015
Water5,368298
1
A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0417
Polymers21,4041
Non-polymers6376
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,19710
Polymers21,4041
Non-polymers7939
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.300, 75.090, 52.760
Angle α, β, γ (deg.)90.00, 93.08, 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: pET-28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00720, lysozyme

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Non-polymers , 6 types, 313 molecules

#2: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical ChemComp-2LP / 2-ALLYLPHENOL


Mass: 134.175 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H10O
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-HED / 2-HYDROXYETHYL DISULFIDE


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.23 Å3/Da / Density % sol: 44.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1 M sodium acetate, pH 4.5, 30% (w/v) PEG-6000, 0.3 M LiSO4, 3% (w/v) TMAO, 50 mM 2-mercaptoethanol, 50 mM 2-hydroxyethyl disulfide, 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: Jun 2, 2012
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: 1.48→43.128 Å / Num. obs: 60993 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 21.865 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 11.96
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.48-1.560.472.24236429073199.4
1.56-1.650.3313.27214738176199.4
1.65-1.770.2234.8222448435198.7
1.77-1.910.1457.29194237335198.4
1.91-2.090.08711.66179746783198
2.09-2.340.05717.06163496176196.9
2.34-2.70.04221.52140105284195.1
2.7-3.310.03325.89116914440193.7
3.31-100.02433.08142865122193.6
10-43.1280.01935450169176.8

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Processing

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

4e97


Resolution: 1.48→43.128 Å / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8903 / SU ML: 0.36 / σ(F): 1.99 / Phase error: 18.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1981 2437 4 %RANDOM
Rwork0.1743 ---
obs0.1753 60991 97.39 %-
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.049 Å2 / ksol: 0.409 e/Å3
Displacement parametersBiso max: 55.44 Å2 / Biso mean: 18.8111 Å2 / Biso min: 5.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.1971 Å2-0 Å21.0694 Å2
2--0.3903 Å20 Å2
3----0.5875 Å2
Refinement stepCycle: LAST / Resolution: 1.48→43.128 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2735 0 82 298 3115
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0212939
X-RAY DIFFRACTIONf_angle_d1.8493979
X-RAY DIFFRACTIONf_chiral_restr0.124439
X-RAY DIFFRACTIONf_plane_restr0.01512
X-RAY DIFFRACTIONf_dihedral_angle_d13.3121087
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.48-1.51020.2731500.23783515366599
1.5102-1.54310.23931390.22283486362599
1.5431-1.5790.24761450.20983498364399
1.579-1.61840.23671470.20193505365299
1.6184-1.66220.22071440.18963503364799
1.6622-1.71110.21641450.18363468361399
1.7111-1.76630.22381410.18243467360898
1.7663-1.82950.23661450.17313495364098
1.8295-1.90270.19371460.16713455360199
1.9027-1.98930.19361460.16553486363298
1.9893-2.09420.19621450.16593452359798
2.0942-2.22540.19011420.16193451359397
2.2254-2.39720.21641420.15983400354296
2.3972-2.63840.20341380.1683355349395
2.6384-3.02010.18591410.18053340348194
3.0201-3.80470.18191380.16433344348294
3.8047-43.1460.16661430.1713334347792
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)
11.07940.27240.33650.6037-0.49720.7370.0378-0.22620.21830.16150.00820.112-0.1433-0.10280.7557-0.06290.01180.0118-0.0368-0.0393-0.05226.554113.16329.9342
20.77090.36210.16640.97780.39790.7663-0.00960.049-0.0439-0.02980.0457-0.01340.0437-0.0061-0.01690.0676-0.0028-0.0120.06670.00770.070830.272619.5356-9.5199
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid -10:206A-10 - 164
2X-RAY DIFFRACTION2chain B and resid -9:209B-9 - 164

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