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- PDB-3sb7: Cu-mediated Trimer of T4 Lysozyme D61H/K65H/R76H/R80H by Syntheti... -

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Basic information

Entry
Database: PDB / ID: 3sb7
TitleCu-mediated Trimer of T4 Lysozyme D61H/K65H/R76H/R80H by Synthetic Symmetrization
ComponentsLysozyme
KeywordsHYDROLASE / metal-mediated synthetic symmetrization / synthetic symmetrization
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
COPPER (II) ION / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsSoriaga, A.B. / Laganowsky, A. / Zhao, M. / Sawaya, M.R. / Cascio, D. / Yeates, T.O.
CitationJournal: Protein Sci. / Year: 2011
Title: An approach to crystallizing proteins by metal-mediated synthetic symmetrization.
Authors: Laganowsky, A. / Zhao, M. / Soriaga, A.B. / Sawaya, M.R. / Cascio, D. / Yeates, T.O.
History
DepositionJun 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2011Group: Derived calculations
Revision 1.2Nov 2, 2011Group: Database references
Revision 1.3Jan 29, 2020Group: Database references / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.biol_id / _struct_ref_seq_dif.details
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)37,3684
Polymers37,2132
Non-polymers1562
Water52229
1
B: Lysozyme
hetero molecules

B: Lysozyme
hetero molecules

B: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0096
Polymers55,8193
Non-polymers1913
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
2
A: Lysozyme
hetero molecules

B: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3684
Polymers37,2132
Non-polymers1562
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_444-y-2/3,x-y-1/3,z-1/31
Buried area1710 Å2
ΔGint-5 kcal/mol
Surface area15470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.910, 119.910, 64.750
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11B-163-

CU

21B-167-

HOH

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Components

#1: Protein Lysozyme / Endolysin / Lysis protein / Muramidase


Mass: 18606.254 Da / Num. of mol.: 2 / Mutation: C54T, D61H, K65H, R76H, R80H, C97A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: E / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P00720, lysozyme
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.41 Å3/Da / Density % sol: 48.91 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 0.2M Potassium Thiocyanate, 25% PEG 3350, vapor diffusion, hanging drop, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 24, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.7→27.472 Å / Num. obs: 9419 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 38.633 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 9.75
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.7-2.770.5083.29219968599.6
2.77-2.850.4463.59220468399
2.85-2.930.3974.29213166899.4
2.93-3.020.2954.942038652100
3.02-3.120.2775.77197161699.4
3.12-3.230.2266.53194959999
3.23-3.350.1667.77185958199.3
3.35-3.490.1369.48181756798.8
3.49-3.640.11510.93172053699.3
3.64-3.820.10411.84166052099
3.82-4.020.08213.33154648698.8
4.02-4.270.07714.3149146498.5
4.27-4.560.0714.97133141998.6
4.56-4.930.07315.28130640299
4.93-5.40.06515.86119737999
5.4-6.040.0714.32104533699.4
6.04-6.970.06415.6994728999
6.97-8.540.04818.6483525398.1
8.54-12.070.04121.3662219297.5
12.070.04921.333059286.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.7 Å27.47 Å
Translation2.7 Å27.47 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→27.472 Å / Occupancy max: 1 / Occupancy min: 0.28 / FOM work R set: 0.8546 / SU ML: 0.68 / σ(F): 2.01 / Phase error: 21.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2261 471 5 %
Rwork0.1866 --
obs0.1885 9417 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.178 Å2 / ksol: 0.343 e/Å3
Displacement parametersBiso max: 83.35 Å2 / Biso mean: 36.2864 Å2 / Biso min: 2.14 Å2
Baniso -1Baniso -2Baniso -3
1--8.0439 Å20 Å20 Å2
2---8.0439 Å20 Å2
3---15.9689 Å2
Refinement stepCycle: LAST / Resolution: 2.7→27.472 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2550 0 7 29 2586
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032604
X-RAY DIFFRACTIONf_angle_d0.5723523
X-RAY DIFFRACTIONf_chiral_restr0.042395
X-RAY DIFFRACTIONf_plane_restr0.002451
X-RAY DIFFRACTIONf_dihedral_angle_d15.195943
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-3.09030.31771560.23382971312799
3.0903-3.89170.24011580.18883004316299
3.8917-27.47360.18111570.16522971312898

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