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- PDB-3g3x: Crystal structure of spin labeled T4 Lysozyme (T151R1) at 100 K -

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Basic information

Entry
Database: PDB / ID: 3g3x
TitleCrystal structure of spin labeled T4 Lysozyme (T151R1) at 100 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 / Lysozyme domain superfamily / Phage lysozyme / 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: 1.8 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 1.3Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Oct 20, 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 1.5Sep 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)19,2398
Polymers18,6301
Non-polymers6097
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.486, 59.486, 95.086
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: 18630.402 Da / Num. of mol.: 1 / Mutation: C54T, C97A, T151R1
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, 169 molecules

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


Mass: 264.385 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H18NO3S2
#3: Chemical ChemComp-HED / 2-HYDROXYETHYL DISULFIDE


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Chemical ChemComp-AZI / AZIDE ION / Azide


Mass: 42.020 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: N3
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.61 Å3/Da / Density % sol: 52.81 %
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: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 15, 2005 / Details: CONFOCAL MIRRORS
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. obs: 18230 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Rsym value: 0.041 / Χ2: 0.913 / Net I/σ(I): 39.199
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3 % / Mean I/σ(I) obs: 6.07 / Num. unique all: 1579 / Rsym value: 0.162 / Χ2: 0.88 / % possible all: 86.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.006data extraction
CrystalCleardata collection
RefinementStarting model: PDB ENTRY 1C6T
Resolution: 1.8→31.695 Å / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.873 / σ(F): 0 / Stereochemistry target values: ml
RfactorNum. reflection% reflectionSelection details
Rfree0.224 935 5.14 %RANDOM
Rwork0.184 ---
all0.186 18612 --
obs0.186 18197 97.77 %-
Solvent computationBsol: 49.436 Å2 / ksol: 0.381 e/Å3
Displacement parametersBiso max: 99.42 Å2 / Biso mean: 17.786 Å2 / Biso min: 7.39 Å2
Baniso -1Baniso -2Baniso -3
1-1.455 Å2-0 Å2-0 Å2
2--1.455 Å20 Å2
3----2.909 Å2
Refinement stepCycle: LAST / Resolution: 1.8→31.695 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1291 0 29 162 1482
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONf_angle_d0.9051
X-RAY DIFFRACTIONf_bond_d0.0041
X-RAY DIFFRACTIONf_chiral_restr0.0531
X-RAY DIFFRACTIONf_dihedral_angle_d16.9511
X-RAY DIFFRACTIONf_plane_restr0.0031
X-RAY DIFFRACTIONf_nbd_refined4.1091
LS refinement shell
Resolution (Å)Rfactor RworkNum. reflection RworkRefine-IDTotal num. of bins used% reflection obs (%)
1.8-1.8170.171397X-RAY DIFFRACTION3577
1.817-1.8350.164421X-RAY DIFFRACTION3581
1.835-1.8540.166447X-RAY DIFFRACTION3586
1.854-1.8740.162457X-RAY DIFFRACTION3586
1.874-1.8950.145455X-RAY DIFFRACTION3588
1.895-1.9160.166483X-RAY DIFFRACTION3591
1.916-1.9390.16459X-RAY DIFFRACTION3590
1.939-1.9620.162483X-RAY DIFFRACTION3594
1.962-1.9870.162504X-RAY DIFFRACTION3592
1.987-2.0130.153464X-RAY DIFFRACTION3593
2.013-2.0410.172520X-RAY DIFFRACTION3594
2.041-2.070.158472X-RAY DIFFRACTION3595
2.07-2.1010.159516X-RAY DIFFRACTION3596
2.101-2.1340.156481X-RAY DIFFRACTION3594
2.134-2.1690.152495X-RAY DIFFRACTION3593
2.169-2.2060.166511X-RAY DIFFRACTION3595
2.206-2.2460.16497X-RAY DIFFRACTION3596
2.246-2.2890.148505X-RAY DIFFRACTION3595
2.289-2.3360.161490X-RAY DIFFRACTION3594
2.336-2.3870.155514X-RAY DIFFRACTION3595
2.387-2.4430.176492X-RAY DIFFRACTION3596
2.443-2.5030.186493X-RAY DIFFRACTION3594
2.503-2.5710.177507X-RAY DIFFRACTION3594
2.571-2.6470.186496X-RAY DIFFRACTION3593
2.647-2.7320.178507X-RAY DIFFRACTION3595
2.732-2.830.213505X-RAY DIFFRACTION3595
2.83-2.9430.206505X-RAY DIFFRACTION3593
2.943-3.0770.201499X-RAY DIFFRACTION3594
3.077-3.2390.19511X-RAY DIFFRACTION3595
3.239-3.4420.167514X-RAY DIFFRACTION3595
3.442-3.7070.161513X-RAY DIFFRACTION3594
3.707-4.0790.154508X-RAY DIFFRACTION3595
4.079-4.6680.16534X-RAY DIFFRACTION3595
4.668-5.8750.178541X-RAY DIFFRACTION3596
5.875-31.70.241566X-RAY DIFFRACTION3594

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