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- PDB-3g3v: Crystal structure of spin labeled T4 Lysozyme (V131R1) at 291 K -

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Basic information

Entry
Database: PDB / ID: 3g3v
TitleCrystal structure of spin labeled T4 Lysozyme (V131R1) at 291 K
ComponentsLysozyme
KeywordsHYDROLASE / MODIFIED CYSTEINE / NITROXIDE / 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 / 2-HYDROXYETHYL DISULFIDE / Chem-MTN / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsFleissner, M.R. / Cascio, D. / Hubbell, W.L.
CitationJournal: 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.
History
DepositionFeb 2, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 27, 2011Group: Non-polymer description
Revision 1.3Oct 20, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / 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 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)19,1997
Polymers18,6321
Non-polymers5676
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.868, 60.868, 96.818
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) / 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 , 5 types, 99 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.: 93 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.73 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 2.0M dibasic potassium phosphate and monobasic sodium phospahte, 0.25M sodium choloride, 0.04% sodium azide, 0.02M oxidized beta-mercaptoehtanol, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 10, 2004
RadiationMonochromator: Confocal Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→80 Å / Num. all: 12597 / Num. obs: 12597 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 20.4 % / Biso Wilson estimate: 23.139 Å2 / Rsym value: 0.123 / Net I/σ(I): 31.19
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 19.4 % / Mean I/σ(I) obs: 8.24 / Num. unique all: 1223 / Rsym value: 0.483 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.006data extraction
CrystalCleardata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementStarting model: PDB ENTRY 1C6T

1c6t


Resolution: 2.1→35.655 Å / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.864 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ml
RfactorNum. reflection% reflectionSelection details
Rfree0.199 611 4.87 %RANDOM
Rwork0.149 ---
all0.1495 12600 --
obs0.1495 12558 99.67 %-
Solvent computationBsol: 62.864 Å2 / ksol: 0.359 e/Å3
Displacement parametersBiso max: 129.27 Å2 / Biso mean: 27.624 Å2 / Biso min: 8.16 Å2
Baniso -1Baniso -2Baniso -3
1-0.728 Å20 Å2-0 Å2
2--0.728 Å20 Å2
3----1.456 Å2
Refinement stepCycle: LAST / Resolution: 2.1→35.655 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1308 0 26 93 1427
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONf_angle_d1.2021
X-RAY DIFFRACTIONf_bond_d0.0071
X-RAY DIFFRACTIONf_chiral_restr0.0681
X-RAY DIFFRACTIONf_dihedral_angle_d18.2421
X-RAY DIFFRACTIONf_plane_restr0.0041
X-RAY DIFFRACTIONf_nbd_refined4.1121
LS refinement shell
Resolution (Å)Rfactor RworkNum. reflection RworkRefine-IDTotal num. of bins used% reflection obs (%)
2.1-2.130.152434X-RAY DIFFRACTION2488
2.13-2.1610.153504X-RAY DIFFRACTION2494
2.161-2.1950.137475X-RAY DIFFRACTION2495
2.195-2.2310.135487X-RAY DIFFRACTION2495
2.231-2.270.123496X-RAY DIFFRACTION2495
2.27-2.3110.126491X-RAY DIFFRACTION2497
2.311-2.3550.144496X-RAY DIFFRACTION2495
2.355-2.4040.145482X-RAY DIFFRACTION2493
2.404-2.4560.141488X-RAY DIFFRACTION2496
2.456-2.5130.137501X-RAY DIFFRACTION2495
2.513-2.5760.141487X-RAY DIFFRACTION2495
2.576-2.6450.152511X-RAY DIFFRACTION2496
2.645-2.7230.184486X-RAY DIFFRACTION2496
2.723-2.8110.182487X-RAY DIFFRACTION2494
2.811-2.9110.159490X-RAY DIFFRACTION2493
2.911-3.0280.16498X-RAY DIFFRACTION2495
3.028-3.1660.168508X-RAY DIFFRACTION2496
3.166-3.3320.154501X-RAY DIFFRACTION2495
3.332-3.5410.148510X-RAY DIFFRACTION2496
3.541-3.8140.131516X-RAY DIFFRACTION2496
3.814-4.1970.126494X-RAY DIFFRACTION2495
4.197-4.8040.123530X-RAY DIFFRACTION2497
4.804-6.0470.145520X-RAY DIFFRACTION2495
6.047-35.660.177555X-RAY DIFFRACTION2494

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