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- PDB-3sb8: Cu-mediated Dimer of T4 Lysozyme D61H/K65H by Synthetic Symmetrization -

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Basic information

Entry
Database: PDB / ID: 3sb8
TitleCu-mediated Dimer of T4 Lysozyme D61H/K65H 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: 2.65 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 1.1Nov 2, 2011Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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
C: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0605
Polymers55,9333
Non-polymers1272
Water21612
1
A: Lysozyme
B: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4164
Polymers37,2892
Non-polymers1272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-28 kcal/mol
Surface area15820 Å2
MethodPISA
2
C: Lysozyme


Theoretical massNumber of molelcules
Total (without water)18,6441
Polymers18,6441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.880, 95.180, 117.020
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 18644.348 Da / Num. of mol.: 3 / Mutation: C54T, D61H, K65H, 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-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 44.95 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 3.5M Sodium Formate, pH 7.0, 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: 2.65→29.441 Å / Num. obs: 14792 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 30.581 Å2 / Rmerge(I) obs: 0.142 / Net I/σ(I): 10.34
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.65-2.720.4813.475788107999.1
2.72-2.790.4393.925821109099.2
2.79-2.870.3864.35533399999.1
2.87-2.960.3285.015430101298.5
2.96-3.060.2875.64519397298.3
3.06-3.170.2366.78504694298.1
3.17-3.290.1987.71485991597.9
3.29-3.420.1569.54470587498.2
3.42-3.570.13311.38442583097.6
3.57-3.750.11512.35425480797.2
3.75-3.950.10513.87399474996.8
3.95-4.190.0915.4385772896.7
4.19-4.480.08216.54363368896.2
4.48-4.840.08316.63314061294.6
4.84-5.30.08816.41311058294.9
5.3-5.930.08815.67283752995.1
5.93-6.840.08516.86253847794.6
6.84-8.380.07119.72212740393.3
8.38-11.850.05423.75160632091.4
11.850.05122.7583418484.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.65 Å29.44 Å
Translation2.65 Å29.44 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: 2.65→29.441 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8001 / SU ML: 0.69 / σ(F): 2.01 / Phase error: 26.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2728 738 5 %
Rwork0.2221 --
obs0.2247 14754 97.24 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 10.276 Å2 / ksol: 0.333 e/Å3
Displacement parametersBiso max: 79.88 Å2 / Biso mean: 27.3026 Å2 / Biso min: 8.64 Å2
Baniso -1Baniso -2Baniso -3
1--3.3243 Å20 Å2-0 Å2
2--2.6923 Å2-0 Å2
3----0.7006 Å2
Refinement stepCycle: LAST / Resolution: 2.65→29.441 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3906 0 2 12 3920
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053975
X-RAY DIFFRACTIONf_angle_d0.7395363
X-RAY DIFFRACTIONf_chiral_restr0.05594
X-RAY DIFFRACTIONf_plane_restr0.002689
X-RAY DIFFRACTIONf_dihedral_angle_d14.5691485
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.65-2.85450.32471480.28212793294199
2.8545-3.14140.31011460.2622788293499
3.1414-3.59530.31691470.23372787293498
3.5953-4.52710.2411480.19572802295097
4.5271-29.44280.22841490.192846299594

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