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- PDB-3sb9: Cu-mediated Dimer of T4 Lysozyme R76H/R80H by Synthetic Symmetrization -

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Basic information

Entry
Database: PDB / ID: 3sb9
TitleCu-mediated Dimer 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 / Lysozyme domain superfamily / Phage lysozyme / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
COPPER (II) ION / FORMIC ACID / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.45 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_seq_id / _struct_conn.ptnr1_label_asym_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

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Assembly

Deposited unit
A: Lysozyme
B: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3045
Polymers37,1482
Non-polymers1563
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-18 kcal/mol
Surface area15290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.114, 79.114, 87.367
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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


Mass: 18574.229 Da / Num. of mol.: 2 / 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-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-CU / COPPER (II) ION / Copper


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


Mass: 18.015 Da / Num. of mol.: 97 / 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: 3.68 Å3/Da / Density % sol: 66.58 %
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: 2.45→80 Å / Num. obs: 19881 / % possible obs: 99.9 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 9.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.45-2.543.60.5291100
2.54-2.643.60.461100
2.64-2.763.60.32199.9
2.76-2.93.60.219199.9
2.9-3.093.60.161199.9
3.09-3.333.60.11199.9
3.33-3.663.60.083199.9
3.66-4.193.60.0791100
4.19-5.283.50.067199.7
5.28-803.50.036199.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å79.11 Å
Translation2.5 Å79.11 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.1.4phasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→79.114 Å / Occupancy max: 1 / Occupancy min: 0.34 / SU ML: 0.74 / σ(F): 0 / Phase error: 25.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2386 1014 5.11 %
Rwork0.1919 --
obs0.1943 19843 99.75 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.893 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.3407 Å20 Å2-0 Å2
2--1.3407 Å2-0 Å2
3----2.6815 Å2
Refinement stepCycle: LAST / Resolution: 2.45→79.114 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2575 0 7 97 2679
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082656
X-RAY DIFFRACTIONf_angle_d1.0743586
X-RAY DIFFRACTIONf_dihedral_angle_d14.771994
X-RAY DIFFRACTIONf_chiral_restr0.065400
X-RAY DIFFRACTIONf_plane_restr0.005459
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.57890.33031410.26562657X-RAY DIFFRACTION100
2.5789-2.74040.36461400.27592719X-RAY DIFFRACTION100
2.7404-2.9520.30161410.24492674X-RAY DIFFRACTION100
2.952-3.24910.26411620.21452663X-RAY DIFFRACTION100
3.2491-3.71930.22071220.18742707X-RAY DIFFRACTION100
3.7193-4.68580.20371700.15072685X-RAY DIFFRACTION100
4.6858-79.15520.20131380.16812724X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 18.3847 Å / Origin y: 20.53 Å / Origin z: -0.5173 Å
111213212223313233
T0.3132 Å2-0.0172 Å20.0218 Å2-0.2504 Å2-0.0004 Å2--0.1768 Å2
L2.3236 °20.2437 °2-0.4655 °2-1.7877 °2-0.5454 °2--1.8114 °2
S-0.0551 Å °0.1224 Å °-0.0256 Å °0.3682 Å °-0.0456 Å °0.0287 Å °0.0225 Å °0.0206 Å °0.1013 Å °
Refinement TLS groupSelection details: ALL

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