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- PDB-4i7q: T4 Lysozyme L99A/M102H with 4-trifluoromethylimidazole bound -

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Basic information

Entry
Database: PDB / ID: 4i7q
TitleT4 Lysozyme L99A/M102H with 4-trifluoromethylimidazole 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
5-(trifluoromethyl)-1H-imidazole / ACETATE ION / BETA-MERCAPTOETHANOL / 2-HYDROXYETHYL DISULFIDE / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 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 1.2Sep 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)44,51320
Polymers42,8092
Non-polymers1,70418
Water5,080282
1
A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,56513
Polymers21,4041
Non-polymers1,16012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9487
Polymers21,4041
Non-polymers5446
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.570, 75.310, 52.650
Angle α, β, γ (deg.)90.00, 93.28, 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, 300 molecules

#2: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical ChemComp-1DQ / 5-(trifluoromethyl)-1H-imidazole


Mass: 136.075 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H3F3N2
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / 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.: 282 / 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: 45.23 %
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: Dec 9, 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: 1.58→48.491 Å / Num. obs: 50444 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 20.165 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 12.64
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.58-1.670.3073.1194387848199.5
1.67-1.780.2094.46187597530199.1
1.78-1.90.1446.32160146386199.3
1.9-2.040.1019.01142955687199
2.04-2.220.06613.41133285268198.1
2.22-2.480.0517.38129485124197
2.48-2.870.04120.8115314548195.3
2.87-3.510.03324.8992673711193.8
3.51-4.960.02532.5473362807191.1
4.96-100.02432.4935921351189.6
10-48.4910.0234.83464184183.6

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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: 1.58→48.491 Å / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.875 / SU ML: 0.35 / σ(F): 1.99 / Phase error: 20.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2132 2033 4.03 %RANDOM
Rwork0.1884 ---
obs0.1894 50441 97.29 %-
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.032 Å2 / ksol: 0.405 e/Å3
Displacement parametersBiso max: 62.24 Å2 / Biso mean: 15.7051 Å2 / Biso min: 3.12 Å2
Baniso -1Baniso -2Baniso -3
1-1.4008 Å2-0 Å20.7147 Å2
2---0.8829 Å20 Å2
3----0.5179 Å2
Refinement stepCycle: LAST / Resolution: 1.58→48.491 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2724 0 94 282 3100
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012937
X-RAY DIFFRACTIONf_angle_d1.2563974
X-RAY DIFFRACTIONf_chiral_restr0.073434
X-RAY DIFFRACTIONf_plane_restr0.005512
X-RAY DIFFRACTIONf_dihedral_angle_d12.2671079
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.58-1.61680.25051330.23713281341499
1.6168-1.65720.2561380.22363280341899
1.6572-1.7020.25461390.221832963435100
1.702-1.75210.26681370.21073278341599
1.7521-1.80860.22811420.20283248339099
1.8086-1.87330.21641330.19123297343099
1.8733-1.94830.23481410.19433304344599
1.9483-2.0370.21411280.18823262339099
2.037-2.14440.21171390.18143223336298
2.1444-2.27870.22121420.17823261340398
2.2787-2.45460.21281310.17693212334397
2.4546-2.70160.20161370.18243190332796
2.7016-3.09250.20721290.19143144327395
3.0925-3.8960.18241340.17063092322693
3.896-48.51340.20181300.18533040317090
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)
10.57870.16420.23720.3961-0.28990.4830.0747-0.22830.2520.16740.01780.1619-0.1713-0.11910.3871-0.04780.07230.0233-0.0287-0.0307-0.04926.607313.65319.904
20.56310.15490.04930.60950.21410.49560.00890.0342-0.0385-0.01590.0348-0.00260.04570.0231-0.00720.0375-0.0013-0.00980.03840.00340.039230.606820.3487-9.388
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid -10:212A-10 - 212
2X-RAY DIFFRACTION2chain B and resid -9:206B-9 - 206

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