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- PDB-4i7r: T4 Lysozyme L99A/M102H with 2-(pyrazolo-1-yl) ethanol bound -

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Basic information

Entry
Database: PDB / ID: 4i7r
TitleT4 Lysozyme L99A/M102H with 2-(pyrazolo-1-yl) ethanol 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-(1H-pyrazol-1-yl)ethanol / ACETATE ION / BETA-MERCAPTOETHANOL / 2-HYDROXYETHYL DISULFIDE / 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 1.0Mar 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_leaving_atom_flag / _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)44,35119
Polymers42,8092
Non-polymers1,54217
Water6,035335
1
A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,34911
Polymers21,4041
Non-polymers94410
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0028
Polymers21,4041
Non-polymers5987
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.590, 75.370, 52.630
Angle α, β, γ (deg.)90.000, 93.250, 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, 352 molecules

#2: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical ChemComp-1DU / 2-(1H-pyrazol-1-yl)ethanol


Mass: 112.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H8N2O
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / 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.: 335 / 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: 45.27 %
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: 1.52→48.512 Å / Num. obs: 54399 / % possible obs: 93.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 20.267 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 17.29
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.52-1.60.3353204428056197.2
1.6-1.70.2284.34204767971196.5
1.7-1.820.1546.34191487336195.8
1.82-1.960.1099.2169906387194.6
1.96-2.150.06315.3165556159193.8
2.15-2.40.04422.18145505336192.1
2.4-2.780.03130.79131254765190
2.78-3.40.02339.89105593830188.5
3.4-4.810.01656.6986932967187.2
4.81-48.5120.01460.4847891592183.7

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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→48.512 Å / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.9013 / SU ML: 0.36 / σ(F): 2 / Phase error: 17.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1903 2170 3.99 %RANDOM
Rwork0.1695 ---
obs0.1704 54399 93.4 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.393 Å2 / ksol: 0.386 e/Å3
Displacement parametersBiso max: 47.82 Å2 / Biso mean: 15.1411 Å2 / Biso min: 4.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.8163 Å2-0 Å21.1031 Å2
2---0.0067 Å2-0 Å2
3---0.823 Å2
Refinement stepCycle: LAST / Resolution: 1.52→48.512 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2752 0 86 335 3173
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012952
X-RAY DIFFRACTIONf_angle_d1.2723986
X-RAY DIFFRACTIONf_chiral_restr0.078435
X-RAY DIFFRACTIONf_plane_restr0.006515
X-RAY DIFFRACTIONf_dihedral_angle_d12.941101
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 (%)
1.52-1.55540.24981530.22463586373997
1.5554-1.59430.22521490.20113618376798
1.5943-1.63740.22721550.1923577373297
1.6374-1.68560.23481410.1863590373196
1.6856-1.740.2041540.17193565371996
1.74-1.80220.21241450.17273583372896
1.8022-1.87430.21361460.1673515366195
1.8743-1.95960.22321440.17273511365595
1.9596-2.06290.19641460.16153485363194
2.0629-2.19220.19091410.1583513365493
2.1922-2.36140.1791400.16483421356192
2.3614-2.59910.20291400.16533372351290
2.5991-2.97510.18661380.17453344348290
2.9751-3.74810.171440.16563299344388
3.7481-48.53650.14811340.15733250338485
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)
10.5432-0.06270.12720.79610.18170.7002-0.0038-0.09010.0790.05710.02240.0426-0.0737-0.0455-0.0080.06980.0090.00120.076-0.00420.05076.532513.99310.2337
20.40320.21790.11620.64370.30510.5114-0.00110.0308-0.0327-0.02130.0339-0.00890.0551-0.0035-0.01690.0562-0.0009-0.00680.05910.00450.038730.491520.5648-9.2795
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid -10:210A-10 - 210
2X-RAY DIFFRACTION2chain B and resid -9:207B-9 - 207

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