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- PDB-3sba: Zn-mediated Hexamer of T4 Lysozyme R76H/R80H by Synthetic Symmetr... -

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Basic information

Entry
Database: PDB / ID: 3sba
TitleZn-mediated Hexamer of T4 Lysozyme 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
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.75 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 / 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_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
C: Lysozyme
D: Lysozyme
E: Lysozyme
F: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,67710
Polymers111,4456
Non-polymers2324
Water724
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.470, 137.780, 146.940
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: 18574.229 Da / Num. of mol.: 6 / Mutation: C54T, 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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.52 Å3/Da / Density % sol: 51.17 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.17M Ammonium Acetate, 0.085 Sodium Acetate Trihydrate, 25.5% PEG 4000, 15% Glycerol, pH 4.6, vapor diffusion, hanging drop, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97949 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: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.75→19.765 Å / Num. obs: 29680 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 32.343 Å2 / Rmerge(I) obs: 0.219 / Net I/σ(I): 5.31
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.75-2.820.491.889008361987.9
2.82-2.90.4222.2610051381092.3
2.9-2.980.3862.5910801369493.6
2.98-3.070.3542.9211510373996.1
3.07-3.180.3113.512055360097.5
3.18-3.290.2764.0612630356898
3.29-3.410.2654.7413095345399.6
3.41-3.550.2295.5213373331399.1
3.55-3.710.2136.2113674321199.3
3.71-3.890.216.6213605305399.8
3.89-4.10.2037.0913591292199.7
4.1-4.350.1967.7413305277599.9
4.35-4.650.1957.8212749259999.9
4.65-5.020.1987.68119362407100
5.02-5.50.27.29108812218100
5.5-6.150.2097.11100242018100
6.15-7.10.1927.869155175699.9
7.1-8.70.1958.877672149799.9
8.7-12.30.1749.365851115099.4
12.30.1799.25238047375.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.9 Å62.56 Å
Translation2.9 Å62.56 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→19.765 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8147 / SU ML: 0.4 / σ(F): 2 / Phase error: 25.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2779 1485 5 %
Rwork0.2219 --
obs0.2248 29680 98.95 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 12.803 Å2 / ksol: 0.333 e/Å3
Displacement parametersBiso max: 166.89 Å2 / Biso mean: 35.3116 Å2 / Biso min: 1.45 Å2
Baniso -1Baniso -2Baniso -3
1--6.6477 Å2-0 Å20 Å2
2---6.3257 Å20 Å2
3---12.9733 Å2
Refinement stepCycle: LAST / Resolution: 2.75→19.765 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7762 0 4 4 7770
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037899
X-RAY DIFFRACTIONf_angle_d0.60110653
X-RAY DIFFRACTIONf_chiral_restr0.0451186
X-RAY DIFFRACTIONf_plane_restr0.0021359
X-RAY DIFFRACTIONf_dihedral_angle_d14.292951
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.75-2.83860.39751270.33772407253495
2.8386-2.93970.33191310.28312495262697
2.9397-3.0570.34291330.26192526265999
3.057-3.19560.34041330.25142516264999
3.1956-3.36330.30951340.23412541267599
3.3633-3.57290.29981340.22322559269399
3.5729-3.84690.25061360.211925712707100
3.8469-4.23050.23881360.196825882724100
4.2305-4.83490.26321360.174925932729100
4.8349-6.06210.23371390.212726432782100
6.0621-19.7660.22781460.193927562902100
Refinement TLS params.Method: refined / Origin x: -1.9424 Å / Origin y: -0.2513 Å / Origin z: -1.3333 Å
111213212223313233
T-0.0043 Å2-0.0413 Å20.004 Å2--0.0158 Å20.0405 Å2---0.0031 Å2
L0.0442 °20.0335 °20.0181 °2-0.0389 °2-0.0126 °2--0.0175 °2
S0.0008 Å °0.0316 Å °-0.0069 Å °0.0358 Å °0.056 Å °-0.0618 Å °0.0365 Å °0.0507 Å °0.0673 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA0 - 161
2X-RAY DIFFRACTION1ALLB0 - 162
3X-RAY DIFFRACTION1ALLC0 - 161
4X-RAY DIFFRACTION1ALLD0 - 162
5X-RAY DIFFRACTION1ALLE0 - 162
6X-RAY DIFFRACTION1ALLF0 - 162

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