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- PDB-1zyt: Crystal structure of spin labeled T4 Lysozyme (A82R1) -

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Basic information

Entry
Database: PDB / ID: 1zyt
TitleCrystal structure of spin labeled T4 Lysozyme (A82R1)
ComponentsLysozyme
KeywordsHYDROLASE / NITROXIDE SPIN LABEL / MODIFIED CYSTEINE
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 / 2-HYDROXYETHYL DISULFIDE / Chem-MTN / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / EPR / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsFleissner, M.R. / Cascio, D. / Sawaya, M.R. / Hideg, K. / Hubbell, W.L.
Citation
Journal: Protein Sci. / Year: 2009
Title: Structural origin of weakly ordered nitroxide motion in spin-labeled proteins
Authors: Fleissner, M.R. / Cascio, D. / Hubbell, W.L.
#1: Journal: BIOCHEMISTRY / Year: 2000
Title: Crystal Structures of Spin Labeled T4 Lysozyme Mutants: Implications for the Interpretation of EPR Spectra in Terms of Structure
Authors: Langen, R. / Oh, K.J. / Cascio, D. / Hubbell, W.L.
History
DepositionJun 10, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 15, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Non-polymer description
Revision 1.4Oct 25, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / 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 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2277
Polymers18,6601
Non-polymers5676
Water3,963220
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.293, 60.293, 96.079
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 / T4 Lysozyme / Lysis protein / Muramidase / Endolysin


Mass: 18660.428 Da / Num. of mol.: 1 / Mutation: C54T/C97A/A82C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P00720, lysozyme

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Non-polymers , 5 types, 226 molecules

#2: Chemical ChemComp-MTN / S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate / MTSL


Mass: 264.385 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H18NO3S2
#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.: 3 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
EPR1

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Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: potassium phosphate, sodium phospahte, sodium choloride, sodium azide, oxidized beta-mercaptoehtanol , pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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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: Feb 23, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→80 Å / Num. all: 22885 / Num. obs: 22843 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.3 % / Biso Wilson estimate: 30.8 Å2 / Rsym value: 0.057 / Net I/σ(I): 41.2
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 8.7 % / Mean I/σ(I) obs: 5.98 / Num. unique all: 2244 / Rsym value: 0.314 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1C6T

1c6t


Resolution: 1.7→52.2 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / SU B: 1.725 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. WITH THE EXCEPTION OF C3, THE POSITIONS OF THE ATOMS OF THE NITROXIDE RING OF MTN ARE NOT UNIQUE, AS THOSE PARTICULAR ATOMS WERE NOT ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. WITH THE EXCEPTION OF C3, THE POSITIONS OF THE ATOMS OF THE NITROXIDE RING OF MTN ARE NOT UNIQUE, AS THOSE PARTICULAR ATOMS WERE NOT RESOLVED. THE COORDINATES FOR THOSE ATOMS OF THE NITROXIDE RING WERE DEPOSITED IN A MINIMUM ENERGY CONFIGURATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.20564 1170 5.1 %RANDOM
Rwork0.18612 ---
all0.18709 21652 --
obs0.18709 21652 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.839 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20.11 Å20 Å2
2--0.22 Å20 Å2
3----0.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.096 Å0.103 Å
Luzzati d res low-52.2 Å
Refinement stepCycle: LAST / Resolution: 1.7→52.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1310 0 26 220 1556
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221369
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2861.9751841
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.4945163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.66923.78866
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.60715257
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.6141513
X-RAY DIFFRACTIONr_chiral_restr0.080.2202
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021012
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.20.2675
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.2956
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2149
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.254
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1160.231
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5911.5844
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it1.7173603
X-RAY DIFFRACTIONr_scangle_it2.5474.5533
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 84 -
Rwork0.318 1592 -
obs-1592 100 %

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