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- PDB-2a4t: Crystal structure of spin labeled T4 Lysozyme (V131R7) -

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Basic information

Entry
Database: PDB / ID: 2a4t
TitleCrystal structure of spin labeled T4 Lysozyme (V131R7)
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 / Lysozyme domain superfamily / Phage lysozyme / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
AZIDE ION / 2-HYDROXYETHYL DISULFIDE / Chem-R7A / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 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 (V131R7
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 29, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 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 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.5Aug 23, 2023Group: 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 / 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
Remark 600HETEROGEN THE POSITIONS OF THE ATOMS OF THE NITROXIDE RING OF R7A ARE NOT UNIQUE, AS THOSE ...HETEROGEN THE POSITIONS OF THE ATOMS OF THE NITROXIDE RING OF R7A ARE NOT UNIQUE, AS THOSE PARTICULAR ATOMS WERE NOT RESOLVED IN EITHER CONFORMATION (A OR B). COORDINATES FOR ATOMS OF THE NITROXIDE RING WERE DEPOSITED IN A MINIMUM ENERGY CONFIGURATION.

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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)19,2787
Polymers18,6321
Non-polymers6466
Water4,468248
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.807, 59.807, 95.580
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 / Gene: E / 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, 254 molecules

#2: Chemical ChemComp-R7A / S-[(4-bromo-1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate


Mass: 343.281 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17BrNO3S2
#3: Chemical ChemComp-AZI / AZIDE ION / Azide


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


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 / Water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.65 Å3/Da / Density % sol: 53.56 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: potassium phosphate, sodium phospahte, sodium choloride, sodium azide, oxidized beta-mercaptoehtanol, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 273K

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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 28, 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: 22428 / Num. obs: 22403 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 28.7 Å2 / Rsym value: 0.059 / Χ2: 1.106 / Net I/σ(I): 32.9
Reflection shellResolution: 1.7→1.76 Å / % possible obs: 99.7 % / Redundancy: 6.3 % / Mean I/σ(I) obs: 5.3 / Num. measured obs: 2221 / Num. unique all: 2221 / Rsym value: 0.303 / Χ2: 0.805 / % possible all: 99.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT1.7data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1C6T

1c6t


Resolution: 1.7→51.78 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.934 / SU B: 1.696 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.215 1143 5.1 %RANDOM
Rwork0.179 ---
all0.181 22350 --
obs0.181 22350 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.987 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20.11 Å20 Å2
2--0.22 Å20 Å2
3----0.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.103 Å0.103 Å
Luzzati d res low-51.78 Å
Refinement stepCycle: LAST / Resolution: 1.7→51.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1308 0 27 248 1583
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221385
X-RAY DIFFRACTIONr_angle_refined_deg1.3921.9931865
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.4075163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.8923.59464
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.55215262
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.5181513
X-RAY DIFFRACTIONr_chiral_restr0.0790.2203
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021020
X-RAY DIFFRACTIONr_nbd_refined0.1980.2707
X-RAY DIFFRACTIONr_nbtor_refined0.2980.2967
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2172
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1370.254
X-RAY DIFFRACTIONr_mcbond_it0.5631.5844
X-RAY DIFFRACTIONr_mcangle_it0.9121307
X-RAY DIFFRACTIONr_scbond_it1.7373620
X-RAY DIFFRACTIONr_scangle_it2.6644.5558
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 91 -
Rwork0.302 1527 -
all-1618 -
obs-1527 99.94 %

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