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- PDB-3l2x: Crystal Structure of Spin Labeled T4 Lysozyme Mutant 115-119RX -

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Basic information

Entry
Database: PDB / ID: 3l2x
TitleCrystal Structure of Spin Labeled T4 Lysozyme Mutant 115-119RX
ComponentsLysozyme
KeywordsHYDROLASE / NITROXIDE SPIN LABEL / EPR / MODIFIED CYSTEINE / Antimicrobial / Bacteriolytic enzyme / Glycosidase
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
AZIDE ION / BETA-MERCAPTOETHANOL / 2-HYDROXYETHYL DISULFIDE / Chem-RXR / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFleissner, M.R. / Cascio, D. / Hubbell, W.L.
CitationJournal: To be Published
Title: Crystal Structure of Spin Labeled T4 Lysozyme Mutant 115-119RX
Authors: Fleissner, M.R. / Cascio, D. / Kalai, T. / Hideg, K. / Hubbell, W.L.
History
DepositionDec 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 5, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...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_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1547
Polymers18,5761
Non-polymers5786
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.113, 60.113, 96.655
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 Lysozyme / Lysis protein / Muramidase / Endolysin


Mass: 18576.350 Da / Num. of mol.: 1 / Mutation: C54T, C97A, T115C, R119C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: E, Lysozyme / Plasmid: pHSe5 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P00720, lysozyme

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Non-polymers , 6 types, 164 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-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: N3
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#6: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsEXTENSIVE EPR EXPERIMENTS OF THE DISULFIDE LINKED RXR LIGAND ATTACHED TO T4 LYSOZYME AT DIFFERENT ...EXTENSIVE EPR EXPERIMENTS OF THE DISULFIDE LINKED RXR LIGAND ATTACHED TO T4 LYSOZYME AT DIFFERENT SITES WERE PERFORMED. THE RXR LIGAND IS A STABLE NITROXYL RADICAL IN SOLUTION, WHICH CAN BE DETECTED BY EPR SPECTROSCOPY.

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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: 2.71 Å3/Da / Density % sol: 54.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 2.0M dibasic potassium phosphate and monobasic sodium phosphate, 0.25M sodium chloride, 0.04% sodium azide, saturated with bis(2-hydroxyethyl) disulfide, pH 6.4, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 3, 2004
RadiationMonochromator: CONFOCAL MIRRORS (BLUE OPTICS) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→80 Å / Num. obs: 18829 / % possible obs: 97.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 9.3 % / Rsym value: 0.072 / Χ2: 1.023 / Net I/σ(I): 12.3
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allRsym valueΧ2% possible all
1.8-1.865.515290.4420.65880.9
1.86-1.947.118130.3370.72595.6
1.94-2.039.818910.2520.81499.4
2.03-2.139.918710.1860.95399.4
2.13-2.279.919180.1391.0399.5
2.27-2.4410.119050.1111.10799.4
2.44-2.6910.119170.091.11899.9
2.69-3.0810.119460.071.20299.9
3.08-3.8810.119560.0541.31399.7
3.88-809.720830.040.96399.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.5_2refinement
PDB_EXTRACT3.005data extraction
CrystalCleardata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1C6T

1c6t


Resolution: 1.8→35.419 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.868 / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Stereochemistry target values: ML
Details: THE RXR LIGAND IS DISUFLDE BONDED TO CYS 115 AND CYS 119, AND WAS MODELED IN AT AN OCCUPANCY OF 0.7
RfactorNum. reflection% reflectionSelection details
Rfree0.232 957 5.09 %RANDOM
Rwork0.184 ---
obs0.187 18802 97.47 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.001 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 76.33 Å2 / Biso mean: 21.209 Å2 / Biso min: 8.09 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å2-0 Å2
2--0.34 Å2-0 Å2
3----0.681 Å2
Refinement stepCycle: LAST / Resolution: 1.8→35.419 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1303 0 31 158 1492
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061369
X-RAY DIFFRACTIONf_angle_d1.1161845
X-RAY DIFFRACTIONf_chiral_restr0.055204
X-RAY DIFFRACTIONf_plane_restr0.004235
X-RAY DIFFRACTIONf_dihedral_angle_d16.249523
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.8950.2731210.2082170229184
1.895-2.0140.2431350.1772536267199
2.014-2.170.221450.16425482693100
2.17-2.3880.2341380.16225862724100
2.388-2.7330.2211400.18526172757100
2.733-3.4430.231410.18826172758100
3.443-35.4250.2131370.17427712908100
Refinement TLS params.Method: refined / Origin x: 25.2491 Å / Origin y: -11.2388 Å / Origin z: 9.4138 Å
111213212223313233
T0.0846 Å2-0.0058 Å20.0027 Å2-0.0709 Å20.0014 Å2--0.0823 Å2
L0.113 °20.0672 °20.0811 °2-0.0868 °2-0.0103 °2--0.1271 °2
S-0.002 Å °0.0108 Å °-0.0034 Å °0.0046 Å °0.0094 Å °-0.0392 Å °0.0272 Å °0.0189 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 164
2X-RAY DIFFRACTION1allA1 - 170
3X-RAY DIFFRACTION1allA1 - 328

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