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- PDB-5lwo: Structure of Spin-labelled T4 lysozyme mutant L115C-R119C-R1 at 100K -

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Basic information

Entry
Database: PDB / ID: 5lwo
TitleStructure of Spin-labelled T4 lysozyme mutant L115C-R119C-R1 at 100K
ComponentsEndolysinLysin
KeywordsHYDROLASE / NITROXIDE / SPIN LABEL / T4 LYSOZYME / ELECTRON PARAMAGNETIC RESONANCE / EPR
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
Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Lysozyme-like domain superfamily
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / 2-HYDROXYETHYL DISULFIDE / : / PHOSPHATE ION / Chem-RXR / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.183 Å
AuthorsLoll, B. / Consentius, P. / Gohlke, U. / Mueller, R. / Kaupp, M. / Heinemann, U. / Wahl, M.C. / Risse, T.
CitationJournal: J Phys Chem Lett / Year: 2017
Title: Internal Dynamics of the 3-Pyrroline-N-Oxide Ring in Spin-Labeled Proteins.
Authors: Consentius, P. / Loll, B. / Gohlke, U. / Alings, C. / Muller, C. / Muller, R. / Teutloff, C. / Heinemann, U. / Kaupp, M. / Wahl, M.C. / Risse, T.
History
DepositionSep 18, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2017Group: Database references
Revision 1.2Jun 12, 2019Group: Data collection / Structure summary
Category: audit_author / database_PDB_rev / database_PDB_rev_record
Item: _audit_author.name
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.4Apr 3, 2024Group: Derived calculations / Category: struct_conn / struct_conn_type
Item: _struct_conn.conn_type_id / _struct_conn.id ..._struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,35611
Polymers18,5761
Non-polymers78010
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-36 kcal/mol
Surface area8930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.170, 60.170, 97.720
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 18576.350 Da / Num. of mol.: 1 / Mutation: C54T C97A L118C T115C R119C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Plasmid: pET28b / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P00720, lysozyme

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Non-polymers , 7 types, 284 molecules

#2: Chemical ChemComp-RXR / [2,2,5,5-tetramethyl-3,4-bis(sulfanylmethyl)-2,5-dihydro-1H-pyrrol-1-yl]oxidanyl radical / 3,4-bis(thiomethyl)-2,2,5,5-tetramethyl-1H-Pyrrol-1-yloxyl radical


Mass: 232.386 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H18NOS2
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-HED / 2-HYDROXYETHYL DISULFIDE


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#7: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 2.75 Å3/Da / Density % sol: 55.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 2.0 M NA/K PHOSPHATE, 240 mM NACL, 40 mM 2-HYDROXYETHYL DISULFIDE, PH 6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.3 / Wavelength: 0.8946 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 4, 2015 / Details: Mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8946 Å / Relative weight: 1
ReflectionResolution: 1.18→50 Å / Num. obs: 66752 / % possible obs: 98.9 % / Redundancy: 4.4 % / Biso Wilson estimate: 11.2 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.084 / Net I/σ(I): 10.1
Reflection shellResolution: 1.18→1.25 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.744 / Mean I/σ(I) obs: 1.8 / CC1/2: 0.772 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JDT

5jdt


Resolution: 1.183→18.299 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.34
RfactorNum. reflection% reflection
Rfree0.1637 2098 3.14 %
Rwork0.1405 --
obs0.1412 66718 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.183→18.299 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1303 0 37 274 1614
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121573
X-RAY DIFFRACTIONf_angle_d1.2852147
X-RAY DIFFRACTIONf_dihedral_angle_d11.388639
X-RAY DIFFRACTIONf_chiral_restr0.082230
X-RAY DIFFRACTIONf_plane_restr0.009280
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1826-1.21010.26911310.24884048X-RAY DIFFRACTION95
1.2101-1.24030.24981370.20384215X-RAY DIFFRACTION98
1.2403-1.27390.2191380.18144247X-RAY DIFFRACTION99
1.2739-1.31130.2191380.17094259X-RAY DIFFRACTION99
1.3113-1.35370.16611380.15534241X-RAY DIFFRACTION99
1.3537-1.4020.18221400.15254308X-RAY DIFFRACTION99
1.402-1.45810.17291390.13764286X-RAY DIFFRACTION99
1.4581-1.52450.14981390.11834274X-RAY DIFFRACTION99
1.5245-1.60480.1631410.11454332X-RAY DIFFRACTION100
1.6048-1.70530.14791400.1174335X-RAY DIFFRACTION100
1.7053-1.83680.1671420.12494347X-RAY DIFFRACTION100
1.8368-2.02150.14491420.13284374X-RAY DIFFRACTION100
2.0215-2.31350.15441420.12524386X-RAY DIFFRACTION99
2.3135-2.91280.14821430.13764401X-RAY DIFFRACTION100
2.9128-18.30140.15961480.14684567X-RAY DIFFRACTION99

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