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- PDB-1p6y: T4 LYSOZYME CORE REPACKING MUTANT M120Y/TA -

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Basic information

Entry
Database: PDB / ID: 1p6y
TitleT4 LYSOZYME CORE REPACKING MUTANT M120Y/TA
ComponentsLYSOZYME
KeywordsHYDROLASE / HYDROLASE (O-GLYCOSYL) / T4 LYSOZYME / DESIGNED CORE MUTANT / AUTOMATED PROTEIN DESIGN / PROTEIN ENGINEERING / PROTEIN FOLDING / PROTEIN STABILITY / CORE REPACKING / BACK REVERTANT / DEAD-END ELIMINATION THEOREM / SIDE-CHAIN PACKING / OPTIMIZED ROTAMER COMBINATIONS / ORBIT
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
2-HYDROXYETHYL DISULFIDE / : / PHOSPHATE ION / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsMooers, B.H. / Datta, D. / Baase, W.A. / Zollars, E.S. / Mayo, S.L. / Matthews, B.W.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Repacking the Core of T4 Lysozyme by Automated Design
Authors: Mooers, B.H. / Datta, D. / Baase, W.A. / Zollars, E.S. / Mayo, S.L. / Matthews, B.W.
History
DepositionApr 30, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 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)19,0206
Polymers18,6601
Non-polymers3595
Water3,459192
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.287, 60.287, 95.298
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: 18660.342 Da / Num. of mol.: 1 / Mutation: C54T, C97A, M120Y
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 / Plasmid: PHS1403 / Production host: Escherichia coli (E. coli) / Strain (production host): RR1 / References: UniProt: P00720, lysozyme

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Non-polymers , 5 types, 197 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / 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.: 192 / 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: 2.71 Å3/Da / Density % sol: 54.32 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: K/Na Phosphate, NaCl, BME, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Method: vapor diffusion / Details: Eriksson, A.E., (1993) J.Mol.Biol., 229, 747. / PH range low: 7.1 / PH range high: 6.3
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
20.25 M1reservoirNaCl
32.0 Mphosphate1reservoir
4beta-mercaptoethanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Aug 31, 2001 / Details: mirrors
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.54→22.894 Å / Num. all: 29398 / Num. obs: 29398 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 20.556 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 8.8
Reflection shellResolution: 1.54→1.6 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 2.8 / Num. unique all: 3205 / Rsym value: 0.252 / % possible all: 97.7
Reflection shell
*PLUS
% possible obs: 96 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
TNTrefinement
CCP4(SCALA)data scaling
TNTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1L63

1l63


Resolution: 1.54→22 Å / Isotropic thermal model: TNT / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT
Details: The working set and the test set were not combined in the last cycles of refinement. The overall anisotropic B values are as follows: B11=B12=B22= 1.85, B13=B23=0.0, B33 = -3.69
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1480 5 %RANDOM
Rwork0.186 ---
obs0.189 29397 92 %-
all-29397 --
Solvent computationSolvent model: TNT / Bsol: 148.044 Å2 / ksol: 0.7167 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.85 Å21.85 Å20 Å2
2--1.85 Å20 Å2
3----3.69 Å2
Refinement stepCycle: LAST / Resolution: 1.54→22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1316 0 16 197 1529
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.013
X-RAY DIFFRACTIONt_angle_deg2.381
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_angle_deg / Dev ideal: 2.4

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