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- PDB-3sb5: Zn-mediated Trimer of T4 Lysozyme R125C/E128C by Synthetic Symmet... -

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Basic information

Entry
Database: PDB / ID: 3sb5
TitleZn-mediated Trimer of T4 Lysozyme R125C/E128C 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: 2.46 Å
AuthorsLaganowsky, A. / Soriaga, A.B. / 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 / pdbx_struct_special_symmetry / 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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_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
B: Lysozyme
A: Lysozyme
C: Lysozyme
D: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,91135
Polymers74,1294
Non-polymers1,78231
Water3,441191
1
B: Lysozyme
hetero molecules

B: Lysozyme
hetero molecules

B: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,90027
Polymers55,5973
Non-polymers1,30424
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area7090 Å2
ΔGint-723 kcal/mol
Surface area22180 Å2
MethodPISA
2
A: Lysozyme
hetero molecules

A: Lysozyme
hetero molecules

A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,17730
Polymers55,5973
Non-polymers1,58027
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area7110 Å2
ΔGint-560 kcal/mol
Surface area22440 Å2
MethodPISA
3
C: Lysozyme
hetero molecules

C: Lysozyme
hetero molecules

C: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,47818
Polymers55,5973
Non-polymers88115
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area4340 Å2
ΔGint-449 kcal/mol
Surface area24070 Å2
MethodPISA
4
D: Lysozyme
hetero molecules

D: Lysozyme
hetero molecules

D: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,17730
Polymers55,5973
Non-polymers1,58027
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area6490 Å2
ΔGint-473 kcal/mol
Surface area23240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.970, 128.970, 295.140
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11B-163-

ZN

21B-170-

CL

31A-164-

ZN

41A-169-

CL

51C-164-

ZN

61C-167-

CL

71D-164-

ZN

81D-171-

CL

91D-207-

HOH

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Components

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Protein , 1 types, 4 molecules BACD

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


Mass: 18532.299 Da / Num. of mol.: 4 / Mutation: C54T, C97A, R125C, E128C
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

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Non-polymers , 5 types, 222 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 3.19 Å3/Da / Density % sol: 61.4 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M Magnesium Chloride, 20% PEG 8000, 0.1M TRIS, pH 8.5, 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: 2.45→80 Å / Num. obs: 34697 / % possible obs: 99.9 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.108 / Χ2: 0.959 / Net I/σ(I): 10.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.45-2.548.20.50834130.688199.9
2.54-2.648.40.39134360.6691100
2.64-2.768.50.30834210.6671100
2.76-2.98.80.22834490.6981100
2.9-3.098.90.15634460.6751100
3.09-3.3390.11334640.7151100
3.33-3.6690.08634580.7951100
3.66-4.198.90.07934840.981100
4.19-5.288.70.06635071.022199.9
5.28-808.70.07936192.596199.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å64.49 Å
Translation2.5 Å64.49 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.1.4phasing
BUSTER-TNTBUSTER 2.8.0refinement
PDB_EXTRACT3.1data extraction
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.46→33.5 Å / Cor.coef. Fo:Fc: 0.9419 / Cor.coef. Fo:Fc free: 0.9191 / Occupancy max: 1 / Occupancy min: 0.33 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2304 1738 5.02 %RANDOM
Rwork0.1844 ---
obs0.1868 34621 --
Displacement parametersBiso max: 121.26 Å2 / Biso mean: 43.9078 Å2 / Biso min: 10.46 Å2
Baniso -1Baniso -2Baniso -3
1-0.633 Å20 Å20 Å2
2--0.633 Å20 Å2
3----1.266 Å2
Refine analyzeLuzzati coordinate error obs: 0.288 Å
Refinement stepCycle: LAST / Resolution: 2.46→33.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5080 0 76 191 5347
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1911SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes125HARMONIC2
X-RAY DIFFRACTIONt_gen_planes759HARMONIC5
X-RAY DIFFRACTIONt_it5212HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion697SEMIHARMONIC5
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_contact6112SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5212HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg7032HARMONIC21.09
X-RAY DIFFRACTIONt_omega_torsion2.76
X-RAY DIFFRACTIONt_other_torsion19.12
LS refinement shellResolution: 2.46→2.54 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.2485 136 4.58 %
Rwork0.1978 2833 -
all0.2001 2969 -
Refinement TLS params.Method: refined / Origin x: -42.2759 Å / Origin y: 44.3713 Å / Origin z: 20.0287 Å
111213212223313233
T-0.0833 Å2-0.0339 Å2-0.0241 Å2--0.0488 Å2-0.0114 Å2--0.1038 Å2
L0.1123 °2-0.0192 °20.0773 °2-0.1725 °20.1138 °2--0.6018 °2
S0.0193 Å °0.0063 Å °0.0136 Å °0.0117 Å °0.0328 Å °-0.0998 Å °-0.0583 Å °0.1133 Å °-0.0522 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B0 - 162
2X-RAY DIFFRACTION1A-1 - 162
3X-RAY DIFFRACTION1C-1 - 162
4X-RAY DIFFRACTION1D0 - 162
5X-RAY DIFFRACTION1A - C11 - 164
6X-RAY DIFFRACTION1C1 - 165
7X-RAY DIFFRACTION1D3 - 231
8X-RAY DIFFRACTION1A1 - 165
9X-RAY DIFFRACTION1B1 - 165
10X-RAY DIFFRACTION1A1 - 166
11X-RAY DIFFRACTION1D1 - 165
12X-RAY DIFFRACTION1B1 - 166
13X-RAY DIFFRACTION1D1 - 166
14X-RAY DIFFRACTION1A1 - 167
15X-RAY DIFFRACTION1D1 - 167
16X-RAY DIFFRACTION1B1 - 167
17X-RAY DIFFRACTION1A1 - 168
18X-RAY DIFFRACTION1B1 - 168
19X-RAY DIFFRACTION1D1 - 168
20X-RAY DIFFRACTION1D1 - 170
21X-RAY DIFFRACTION1D1 - 171
22X-RAY DIFFRACTION1A1 - 169
23X-RAY DIFFRACTION1B1 - 170
24X-RAY DIFFRACTION1C1 - 167
25X-RAY DIFFRACTION1A1 - 170
26X-RAY DIFFRACTION1A1 - 171

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