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- PDB-1zwn: Crystal structure of spin labeled T4 Lysozyme (V131R1B) -

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Basic information

Entry
Database: PDB / ID: 1zwn
TitleCrystal structure of spin labeled T4 Lysozyme (V131R1B)
ComponentsLysozyme
KeywordsHYDROLASE / Nitroxide spin label / EPR / 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-R1B / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFleissner, M.R. / Cascio, D. / Sawaya, M.R. / Hideg, K. / Hubbell, W.L.
Citation
Journal: To be Published
Title: Crystal structure of spin labeled T4 Lysozyme (V131R1B)
Authors: Fleissner, M.R. / Cascio, D. / Sawaya, M.R. / Hideg, K. / 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 3, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 17, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 29, 2012Group: Other
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 16, 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)19,2558
Polymers18,6321
Non-polymers6237
Water3,855214
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.793, 59.793, 95.442
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: 18632.375 Da / Num. of mol.: 1 / Mutation: C54T, C97A, V131C
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, 221 molecules

#2: Chemical ChemComp-R1B / S-[(1-oxyl-2,2,4,5,5-pentamethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate


Mass: 278.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H20NO3S2
#3: Chemical ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 2 / 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.: 214 / 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

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.47 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: potassium phosphate, sodium phospahte, sodium choloride, sodium azide, oxidized beta-mercaptoehtanol, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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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: Aug 1, 2002
RadiationProtocol: 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. all: 18924 / Num. obs: 17382 / % possible obs: 91.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 17.26 % / Biso Wilson estimate: 27.6 Å2 / Rsym value: 0.085 / Net I/σ(I): 34.9
Reflection shellResolution: 1.8→1.86 Å / Mean I/σ(I) obs: 34.9 / Num. unique all: 1084 / Rsym value: 0.423 / % possible all: 58.5

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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: 1.8→51.99 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.922 / SU B: 2.166 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.138 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22212 889 5.1 %RANDOM
Rwork0.18431 ---
all0.18615 16493 --
obs0.18615 16493 91.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.932 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20.05 Å20 Å2
2--0.09 Å20 Å2
3----0.14 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.13 Å0.138 Å
Luzzati d res low-51.99 Å
Refinement stepCycle: LAST / Resolution: 1.8→51.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1308 0 30 214 1552
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221401
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.741.9921883
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.4325163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.29723.28467
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.41215270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.6981515
X-RAY DIFFRACTIONr_chiral_restr0.0810.2203
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021034
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1850.2681
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2840.2967
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1110.2167
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.267
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0860.234
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4021.5853
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.64121309
X-RAY DIFFRACTIONr_scbond_it1.2093640
X-RAY DIFFRACTIONr_scangle_it1.7524.5574
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.845 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.414 55 -
Rwork0.335 711 -
obs--55.99 %

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