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- PDB-3sb6: Cu-mediated Dimer of T4 Lysozyme D61H/K65H/R76H/R80H by Synthetic... -

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Basic information

Entry
Database: PDB / ID: 3sb6
TitleCu-mediated Dimer 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 / Lysozyme domain superfamily / Phage lysozyme / 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 / 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 1.1Nov 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 / _pdbx_struct_conn_angle.value / _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_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4116
Polymers37,2132
Non-polymers1984
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-47 kcal/mol
Surface area16700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.040, 69.840, 89.040
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: 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-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.51 Å3/Da / Density % sol: 50.96 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 0.2M Ammonium Nitrate, 20% PEG 3350, vapor diffusion, hanging drop, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 8, 2010
RadiationMonochromator: CONFOCAL VARIMAX HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 10710 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 54.578 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 15.84
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.7-2.770.5533.415582781100
2.77-2.850.4624.045486765100
2.85-2.930.4114.68516272299.9
2.93-3.020.3275.695161721100
3.02-3.120.277.14993695100
3.12-3.230.2258.52481967499.7
3.23-3.350.16111.264690657100
3.35-3.490.12114.44520631100
3.49-3.640.10417.38430260299.7
3.64-3.820.0822.124134585100
3.82-4.030.0820.92395756399.8
4.03-4.270.06325.47369452299.6
4.27-4.560.06426.92343249299.6
4.56-4.930.06325.26325346399.6
4.93-5.40.0627.653006435100
5.4-6.040.06724.682708395100
6.04-6.970.05827.292358347100
6.97-8.540.04334.982054308100
8.54-12.080.03738.421534242100
12.080.03440.6965311074.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.95 Å19.99 Å
Translation2.95 Å19.99 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
BUSTER-TNTBUSTER 2.8.0refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.9214 / Cor.coef. Fo:Fc free: 0.8753 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2717 954 8.91 %RANDOM
Rwork0.2261 ---
obs0.2301 10710 --
Displacement parametersBiso max: 149.13 Å2 / Biso mean: 60.4836 Å2 / Biso min: 24.2 Å2
Baniso -1Baniso -2Baniso -3
1-4.6588 Å20 Å20 Å2
2--5.4151 Å20 Å2
3----10.0738 Å2
Refine analyzeLuzzati coordinate error obs: 0.505 Å
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2536 0 4 24 2564
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d925SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes67HARMONIC2
X-RAY DIFFRACTIONt_gen_planes379HARMONIC5
X-RAY DIFFRACTIONt_it2585HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion348SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2898SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2585HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg3504HARMONIC20.94
X-RAY DIFFRACTIONt_omega_torsion1.84
X-RAY DIFFRACTIONt_other_torsion17.79
LS refinement shellResolution: 2.7→3.02 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3128 252 8.44 %
Rwork0.2642 2734 -
all0.2681 2986 -
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)
14.2104-2.6633-1.23235.09060.84561.6664-0.1526-0.1553-0.0244-0.36330.3081-0.19410.08090.3676-0.1555-0.117-0.01920.068-0.1247-0.075-0.0998-17.3216-12.174612.1862
24.9379-0.9077-2.16453.7360.92611.94180.1113-0.27620.20020.27-0.0750.1712-0.1523-0.0933-0.0363-0.19510.03770.0343-0.11940.0106-0.0783-45.7573-22.686728.0265
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 165
2X-RAY DIFFRACTION2B2 - 165

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