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- PDB-4i7k: T4 Lysozyme L99A/M102H with toluene bound -

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Basic information

Entry
Database: PDB / ID: 4i7k
TitleT4 Lysozyme L99A/M102H with toluene 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 / TOLUENE / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 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.pdbx_ptnr2_label_alt_id / _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

Downloads & links

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Assembly

Deposited unit
A: Lysozyme
B: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,33320
Polymers42,8092
Non-polymers1,52418
Water5,855325
1
A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1549
Polymers21,4041
Non-polymers7508
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,17811
Polymers21,4041
Non-polymers77410
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.320, 75.550, 52.760
Angle α, β, γ (deg.)90.000, 93.210, 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, 343 molecules

#2: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical ChemComp-MBN / TOLUENE


Mass: 92.138 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8
#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.: 4 / 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.: 325 / 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: 45.24 %
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: 1.72→48.244 Å / Num. obs: 39518 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 21.122 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 13.01
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.72-1.810.3583.01142245622199.2
1.81-1.920.2674.15141695572199.4
1.92-2.050.1776.12129955085199.1
2.05-2.220.1139.28128224971198.9
2.22-2.430.07712.87113924398198.6
2.43-2.720.05616.45104954019198.2
2.72-3.140.04620.0290883464197.2
3.14-3.850.03227.6676082912195.5
3.85-5.440.02435.2360172243195.4
5.44-100.02335.8128091030194.2
10-48.2440.01941.15539202191.8

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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: 1.72→48.244 Å / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8879 / SU ML: 0.38 / σ(F): 1.99 / Phase error: 18.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2005 1570 3.97 %RANDOM
Rwork0.1679 ---
obs0.1692 39514 98.15 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.004 Å2 / ksol: 0.366 e/Å3
Displacement parametersBiso max: 53.32 Å2 / Biso mean: 15.4172 Å2 / Biso min: 2.17 Å2
Baniso -1Baniso -2Baniso -3
1--0.917 Å2-0 Å20.2029 Å2
2---0.0099 Å2-0 Å2
3---0.9269 Å2
Refinement stepCycle: LAST / Resolution: 1.72→48.244 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2745 0 87 325 3157
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123003
X-RAY DIFFRACTIONf_angle_d1.1464059
X-RAY DIFFRACTIONf_chiral_restr0.076440
X-RAY DIFFRACTIONf_plane_restr0.005529
X-RAY DIFFRACTIONf_dihedral_angle_d12.7461117
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.72-1.77560.28621450.23573482362799
1.7756-1.8390.22931450.20413462360799
1.839-1.91270.23541440.18043474361899
1.9127-1.99970.21551410.1693481362299
1.9997-2.10510.1841450.15273469361499
2.1051-2.2370.19481420.14723464360699
2.237-2.40970.1861430.15163453359698
2.4097-2.65220.20891440.15523439358398
2.6522-3.0360.19591450.16783437358297
3.036-3.82470.17721400.16293377351796
3.8247-48.26290.19451360.17383406354295
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)
10.44010.12640.14320.3226-0.27460.40020.0757-0.14720.17340.17010.03920.1221-0.1763-0.07410.505-0.08320.05750.0795-0.0616-0.0724-0.11066.504314.860310.2785
20.37550.1870.1090.3630.10840.29130.01240.0308-0.0548-0.00980.05140.00380.0792-0.00070.00150.0467-0.0069-0.00660.0460.00460.051430.275121.297-9.4369
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid -10:208A-10 - 164
2X-RAY DIFFRACTION2chain B and resid -10:209B-10 - 164

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