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- PDB-3hwl: Crystal Structure of T4 lysozyme with the unnatural amino acid p-... -

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Basic information

Entry
Database: PDB / ID: 3hwl
TitleCrystal Structure of T4 lysozyme with the unnatural amino acid p-Acetyl-L-Phenylalanine incorporated at position 131
ComponentsLysozyme
KeywordsHYDROLASE / UNNATURAL AMINO ACID / p-ACETYL-PHENYLALANINE / 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 / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFleissner, M.R. / Cascio, D. / Schultz, P.G. / Hubbell, W.L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Site-directed spin labeling of a genetically encoded unnatural amino acid.
Authors: Fleissner, M.R. / Brustad, E.M. / Kalai, T. / Altenbach, C. / Cascio, D. / Peters, F.B. / Hideg, K. / Peuker, S. / Schultz, P.G. / Hubbell, W.L.
History
DepositionJun 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 10, 2011Group: Database references
Revision 1.3Oct 13, 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id
Revision 2.1Dec 27, 2023Group: Derived calculations / Category: struct_conn

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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)18,9306
Polymers18,7401
Non-polymers1905
Water2,342130
1
A: Lysozyme
hetero molecules

A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,86012
Polymers37,4792
Non-polymers38110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area3160 Å2
ΔGint-46 kcal/mol
Surface area15950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.972, 59.972, 96.282
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Lysozyme / / Lysis protein / Muramidase / Endolysin


Mass: 18739.549 Da / Num. of mol.: 1 / Mutation: C54T,C97A,N68C,A93C,V131(4AF)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: E, LYSOZYME / Plasmid: PET101/D-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00720, lysozyme
#2: Chemical ChemComp-AZI / AZIDE ION / Azide


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


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


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.67 Å3/Da / Density % sol: 53.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 2.0M sodium/potassium phosphate, 0.2M sodium chloride, 0.04% sodium azide, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 12, 2008
RadiationMonochromator: CONFOCAL MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→51.94 Å / Num. all: 19132 / Num. obs: 19132 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 14.4 % / Biso Wilson estimate: 34.8 Å2 / Rsym value: 0.085 / Net I/σ(I): 30.4
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 15.2 % / Mean I/σ(I) obs: 10.6 / Num. unique all: 1883 / Rsym value: 0.384 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIX(phenix.refine)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L63

1l63


Resolution: 1.8→35.307 Å / SU ML: 0.22 / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1.89 / Stereochemistry target values: ML
Details: THE STRUCTURAL DATA ARE CONSISTENT WITH THE P-ACETYL-L-PHENYLALANINE SIDE CHAIN MODELED, AS WELL AS A SECOND ROTAMER WHEREIN THE TORSIONAL ANGLE DEFINED BY THE ATOMS C6-C7-C8-O2 IS 180 DEGREES
RfactorNum. reflection% reflectionSelection details
Rfree0.2268 981 5.14 %RANDOM
Rwork0.1866 ---
all0.1885 19090 --
obs0.1885 19090 53.17 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.205 Å2 / ksol: 0.385 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.5057 Å20 Å20 Å2
2--2.5057 Å20 Å2
3----5.0113 Å2
Refinement stepCycle: LAST / Resolution: 1.8→35.307 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1292 0 9 130 1431
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061326
X-RAY DIFFRACTIONf_angle_d0.9151785
X-RAY DIFFRACTIONf_chiral_restr0.06198
X-RAY DIFFRACTIONf_plane_restr0.003228
X-RAY DIFFRACTIONf_dihedral_angle_d15.32494
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.89510.24721480.17812531X-RAY DIFFRACTION52
1.8951-2.01380.23581580.16942521X-RAY DIFFRACTION52
2.0138-2.16930.20241340.16132564X-RAY DIFFRACTION53
2.1693-2.38750.20311330.15912573X-RAY DIFFRACTION53
2.3875-2.73290.21941380.18852593X-RAY DIFFRACTION53
2.7329-3.44270.26981300.19762608X-RAY DIFFRACTION53
3.4427-35.31350.20071400.17772719X-RAY DIFFRACTION56
Refinement TLS params.Method: refined / Origin x: 34.716 Å / Origin y: 11.2567 Å / Origin z: 9.193 Å
111213212223313233
T0.1665 Å20.0019 Å20.0018 Å2-0.1529 Å20.0006 Å2--0.1641 Å2
L0.0949 °20.1195 °2-0.1267 °2-0.1406 °2-0.036 °2--0.1104 °2
S0.0148 Å °0.0068 Å °0.0219 Å °0.0136 Å °0.0049 Å °0.0319 Å °-0.0444 Å °0.0019 Å °0 Å °
Refinement TLS groupSelection details: all

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