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- PDB-4e97: T4 Lysozyme L99A/M102H with 2-Mercaptoethanol Bound -

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Open data


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Basic information

Entry
Database: PDB / ID: 4.0E+97
TitleT4 Lysozyme L99A/M102H with 2-Mercaptoethanol Bound
ComponentsLysozyme
KeywordsHYDROLASE / Alkylation with 2-mercaptoethanol
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 / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å
AuthorsMerski, M. / Shoichet, B.K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Engineering a model protein cavity to catalyze the Kemp elimination.
Authors: Merski, M. / Shoichet, B.K.
History
DepositionMar 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Database references
Revision 1.2Oct 17, 2012Group: Database references
Revision 1.3Oct 31, 2012Group: Structure summary
Revision 1.4Sep 13, 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_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_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)44,18718
Polymers42,8092
Non-polymers1,37816
Water7,440413
1
A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,23810
Polymers21,4041
Non-polymers8339
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9498
Polymers21,4041
Non-polymers5457
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.300, 75.420, 52.600
Angle α, β, γ (deg.)90.000, 93.400, 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 , 5 types, 429 molecules

#2: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-HED / 2-HYDROXYETHYL DISULFIDE


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 413 / 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: 2.23 Å3/Da / Density % sol: 44.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1 M sodium acetate, 30% (w/v) PEG-6000, 0.3 M LiSO4, 3% (w/v) TMAO, 50 mM 2-mercaptoethanol, 50 mM 2-hydroxyethyl disulfide, pH 4.5, 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: Aug 25, 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: 1.3→50 Å / Num. obs: 92251 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 17.456 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 19.18
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.3-1.360.4872.814127111609199.8
1.36-1.440.3484.115417412627199.8
1.44-1.540.2278.4389599123681100
1.54-1.670.14712.4887596119701100
1.67-1.850.09418.484567115011100
1.85-2.150.06227.3585178116271100
2.15-2.540.04438.626017480541100
2.54-3.590.03745.02595178031199.9
3.59-500.03151.29314454464199.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å48.22 Å
Translation2.5 Å48.22 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 181L

181l


Resolution: 1.3→48.215 Å / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.9311 / SU ML: 0.31 / σ(F): 2 / Phase error: 13.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1655 3690 4 %RANDOM
Rwork0.142 ---
obs0.1429 92247 99.9 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.05 Å2 / ksol: 0.391 e/Å3
Displacement parametersBiso max: 50.49 Å2 / Biso mean: 14.9849 Å2 / Biso min: 4.68 Å2
Baniso -1Baniso -2Baniso -3
1--0.9064 Å2-0 Å2-0.4321 Å2
2---1.226 Å2-0 Å2
3---2.1324 Å2
Refinement stepCycle: LAST / Resolution: 1.3→48.215 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2775 0 73 413 3261
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143142
X-RAY DIFFRACTIONf_angle_d1.4784271
X-RAY DIFFRACTIONf_chiral_restr0.097465
X-RAY DIFFRACTIONf_plane_restr0.009559
X-RAY DIFFRACTIONf_dihedral_angle_d13.2611226
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3-1.31710.25181410.209233933534100
1.3171-1.33520.19181410.180333863527100
1.3352-1.35420.18231410.166633853526100
1.3542-1.37440.19921420.161733963538100
1.3744-1.39590.211390.154533513490100
1.3959-1.41880.1961430.153534323575100
1.4188-1.44330.15421420.147133963538100
1.4433-1.46950.18791410.1333973538100
1.4695-1.49780.16371400.120533643504100
1.4978-1.52840.15681420.116534123554100
1.5284-1.56160.16821420.114734063548100
1.5616-1.59790.14531440.110634383582100
1.5979-1.63790.15051400.106333713511100
1.6379-1.68220.13241420.109934003542100
1.6822-1.73170.14331420.104634173559100
1.7317-1.78760.15111420.112334013543100
1.7876-1.85150.15051410.116533953536100
1.8515-1.92560.16261420.122734123554100
1.9256-2.01320.15161430.134534133556100
2.0132-2.11940.16041410.134533973538100
2.1194-2.25220.17221420.137934033545100
2.2522-2.4260.17261440.1434463590100
2.426-2.67020.1871420.152334123554100
2.6702-3.05650.16431430.16134333576100
3.0565-3.85060.14771430.1534363579100
3.8506-48.24830.16941450.1643465361099

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