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- PDB-4i7l: T4 Lysozyme L99A/M102H with phenol bound -

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Basic information

Entry
Database: PDB / ID: 4i7l
TitleT4 Lysozyme L99A/M102H with phenol 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
ACETATE ION / BETA-MERCAPTOETHANOL / 2-HYDROXYETHYL DISULFIDE / PHENOL / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 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 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2013Group: Database references
Revision 1.2Sep 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_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)44,19918
Polymers42,8092
Non-polymers1,39116
Water6,359353
1
A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,29311
Polymers21,4041
Non-polymers88910
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9067
Polymers21,4041
Non-polymers5026
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.440, 75.370, 52.680
Angle α, β, γ (deg.)90.000, 93.310, 90.000
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, 369 molecules

#2: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical ChemComp-IPH / PHENOL


Mass: 94.111 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H6O
#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.: 353 / 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: 2.24 Å3/Da / Density % sol: 45.15 %
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: Oct 20, 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: 1.52→48.359 Å / Num. obs: 56081 / % possible obs: 96.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 19.296 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 15.01
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.52-1.60.313.12204918171198.5
1.6-1.70.2264.37204238085198.3
1.7-1.820.1556.28191957506198
1.82-1.990.1029.26200037741197.5
1.99-2.20.06215.04169826520197
2.2-2.490.04321.22150695699195.8
2.49-2.960.03326.64134065058194.5
2.96-3.580.02435.9886373170192
3.58-4.780.01847.0867622408192.2
4.78-100.01746.4943751535189.7
10-48.3590.01451.86513188185.5

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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: 1.52→48.359 Å / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.9101 / SU ML: 0.31 / σ(F): 1.99 / Phase error: 16.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1808 2247 4.01 %RANDOM
Rwork0.161 ---
obs0.1618 56080 96.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.496 Å2 / ksol: 0.384 e/Å3
Displacement parametersBiso max: 53.78 Å2 / Biso mean: 14.8848 Å2 / Biso min: 3.61 Å2
Baniso -1Baniso -2Baniso -3
1-0.334 Å20 Å2-0.2795 Å2
2--0.0994 Å20 Å2
3----0.4333 Å2
Refinement stepCycle: LAST / Resolution: 1.52→48.359 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2744 0 79 353 3176
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132978
X-RAY DIFFRACTIONf_angle_d1.4454023
X-RAY DIFFRACTIONf_chiral_restr0.086439
X-RAY DIFFRACTIONf_plane_restr0.007521
X-RAY DIFFRACTIONf_dihedral_angle_d12.7781103
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.52-1.55310.22511470.23415356299
1.5531-1.58920.2421420.19383400354298
1.5892-1.6290.20111460.18093439358599
1.629-1.6730.20981450.17553424356998
1.673-1.72220.20211380.16593397353598
1.7222-1.77780.20271380.16363406354498
1.7778-1.84140.19231440.15613412355698
1.8414-1.91510.18971480.15713386353498
1.9151-2.00230.17721380.15263384352297
2.0023-2.10780.16731400.15313404354497
2.1078-2.23990.18821400.14673354349497
2.2399-2.41280.16831440.15033335347996
2.4128-2.65560.20771350.15983320345595
2.6556-3.03980.14921380.17053296343494
3.0398-3.82960.16941340.15423223335792
3.8296-48.38370.16031300.15953238336891
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)
10.5820.15640.23860.4222-0.33060.50640.0065-0.11840.1170.10520.01070.0796-0.101-0.07720.2519-0.03140.02310.0213-0.0234-0.0129-0.04176.569415.251410.0956
20.49820.25110.16620.66750.30640.53610.00280.0233-0.0347-0.00710.02810.00420.0562-0.0127-0.01640.0441-0.00370.00150.04950.00610.048230.46621.8966-9.2163
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid -11:210A-11 - 164
2X-RAY DIFFRACTION2chain B and resid -10:206B-10 - 164

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