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- PDB-4i7t: T4 Lysozyme L99A/M102H with 2-bromo-5-hydroxybenzaldehyde bound -

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Basic information

Entry
Database: PDB / ID: 4i7t
TitleT4 Lysozyme L99A/M102H with 2-bromo-5-hydroxybenzaldehyde 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-bromo-5-hydroxybenzaldehyde / ACETATE ION / BETA-MERCAPTOETHANOL / 2-HYDROXYETHYL DISULFIDE / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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)44,27616
Polymers42,8092
Non-polymers1,46714
Water5,765320
1
A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2639
Polymers21,4041
Non-polymers8598
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0137
Polymers21,4041
Non-polymers6086
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.060, 75.810, 52.710
Angle α, β, γ (deg.)90.000, 93.110, 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, 334 molecules

#2: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical ChemComp-1DW / 2-bromo-5-hydroxybenzaldehyde


Mass: 201.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H5BrO2
#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.: 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.: 320 / 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: 45.08 %
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: 1.55→47.989 Å / Num. obs: 52337 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 21.494 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 14.85
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.55-1.630.3673.07162846987192.3
1.63-1.730.264.83193877596198.9
1.73-1.850.1837.02182407083198.6
1.85-20.11710.5170496557198
2-2.190.0715.9154535914197.4
2.19-2.450.0521.02140415325196.4
2.45-2.830.03925.38123484634194.9
2.83-3.470.03129.89102573833192.6
3.47-100.02536.83114914239189.4
10-47.9890.02438.4432169176.5

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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: 1.55→47.989 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.892 / SU ML: 0.42 / σ(F): 1.99 / Phase error: 18.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1985 2103 4.02 %RANDOM
Rwork0.1747 ---
obs0.1757 52336 95.66 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.558 Å2 / ksol: 0.39 e/Å3
Displacement parametersBiso max: 55.96 Å2 / Biso mean: 16.6634 Å2 / Biso min: 3.61 Å2
Baniso -1Baniso -2Baniso -3
1--1.6965 Å20 Å2-0.3838 Å2
2--1.7092 Å2-0 Å2
3----0.0127 Å2
Refinement stepCycle: LAST / Resolution: 1.55→47.989 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2743 0 77 320 3140
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0213010
X-RAY DIFFRACTIONf_angle_d1.9414079
X-RAY DIFFRACTIONf_chiral_restr0.142444
X-RAY DIFFRACTIONf_plane_restr0.011528
X-RAY DIFFRACTIONf_dihedral_angle_d13.4811145
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 (%)
1.55-1.58610.25661320.2842962309486
1.5861-1.62570.30081370.25953410354797
1.6257-1.66970.27061430.23613460360399
1.6697-1.71880.25641440.21153453359799
1.7188-1.77430.22111490.19333457360699
1.7743-1.83770.20761370.17463413355099
1.8377-1.91130.19761460.16633436358298
1.9113-1.99830.18951400.16153422356298
1.9983-2.10360.20521390.16433437357698
2.1036-2.23540.191440.16173391353597
2.2354-2.4080.19731440.15873360350496
2.408-2.65030.21381420.16133354349695
2.6503-3.03380.18971380.1713287342594
3.0338-3.8220.16211370.15983227336492
3.822-48.01230.1761310.17053164329588
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)
10.60830.17180.1490.3086-0.29940.50630.1458-0.19540.18880.1230.04130.1466-0.1512-0.07480.698-0.04980.06390.0388-0.0313-0.0557-0.05066.562714.26210.2181
20.50240.34120.15460.62130.28630.65870.01330.0385-0.0338-0.00840.0467-0.00330.0605-0.0156-0.03160.0465-0.0019-0.00280.0450.00820.053529.992420.9144-9.3926
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid -10:208A-10 - 208
2X-RAY DIFFRACTION2chain B and resid -9:206B-9 - 206

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