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- PDB-262l: STRUCTURAL CHARACTERISATION OF AN ENGINEERED TANDEM REPEAT CONTRA... -

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Basic information

Entry
Database: PDB / ID: 262l
TitleSTRUCTURAL CHARACTERISATION OF AN ENGINEERED TANDEM REPEAT CONTRASTS THE IMPORTANCE OF CONTEXT AND SEQUENCE IN PROTEIN FOLDING
ComponentsLYSOZYME
KeywordsHYDROLASE / HYDROLASE (O-GLYCOSYL) / T4 LYSOZYME / ENGINEERED TANDEM REPEAT / PROTEIN ENGINEERING / PROTEIN DESIGN
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
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSagermann, M. / Baase, W.A. / Matthews, B.W.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Structural characterization of an engineered tandem repeat contrasts the importance of context and sequence in protein folding.
Authors: Sagermann, M. / Baase, W.A. / Matthews, B.W.
#1: Journal: Protein Sci. / Year: 1998
Title: Protein Structural Plasticity Examplified by Insertion and Deletion
Authors: Vetter, I.R. / Baase, W.A. / Heinz, D. / Xiong, J.P. / Snow, S. / Matthews, B.W.
#2: Journal: Nature / Year: 1993
Title: Folding and Function of a T4 Lysosyme Containing 10 Consecutive Alanines Illustrate the Redundancy of Information in an Amino Acid Sequence
Authors: Heinz, D. / Baase, W.A. / Dahlquist, F.W. / Matthews, B.W.
History
DepositionMay 11, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0May 24, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 26, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software
Revision 1.5Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.6Dec 19, 2018Group: Data collection / Structure summary / Category: entity / struct / struct_keywords
Item: _entity.pdbx_description / _entity.pdbx_mutation ..._entity.pdbx_description / _entity.pdbx_mutation / _struct.pdbx_descriptor / _struct_keywords.pdbx_keywords / _struct_keywords.text
Revision 1.7Jul 22, 2020Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: diffrn / diffrn_detector ...diffrn / diffrn_detector / diffrn_radiation / diffrn_source / pdbx_database_status / software / struct_ref_seq_dif
Item: _diffrn.ambient_pressure / _diffrn.ambient_temp ..._diffrn.ambient_pressure / _diffrn.ambient_temp / _diffrn_detector.details / _diffrn_detector.type / _diffrn_radiation.pdbx_wavelength_list / _diffrn_source.source / _diffrn_source.target / _pdbx_database_status.status_code_sf / _software.name / _struct_ref_seq_dif.details
Revision 1.8Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.9Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LYSOZYME
B: LYSOZYME


Theoretical massNumber of molelcules
Total (without water)39,0892
Polymers39,0892
Non-polymers00
Water1,76598
1
A: LYSOZYME


Theoretical massNumber of molelcules
Total (without water)19,5441
Polymers19,5441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LYSOZYME


Theoretical massNumber of molelcules
Total (without water)19,5441
Polymers19,5441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.720, 55.790, 65.180
Angle α, β, γ (deg.)90.00, 110.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein LYSOZYME


Mass: 19544.395 Da / Num. of mol.: 2 / Mutation: L39I
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
Description: BACTERIOPHAGE T4 (MUTANT GENE DERIVED FROM THE M13 PLASMID BY CLONING THE T4 LY SOZYME GENE)
Cellular location: CYTOPLASM / Gene: GENE E FROM BACTERIOPHAGE T4 / Plasmid: PHS1403 / Gene (production host): T4 LYSOZYME / Production host: Escherichia coli (E. coli) / Strain (production host): RR1 / References: UniProt: P00720, lysozyme
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.72 Å3/Da / Density % sol: 54 %
Crystal growpH: 7.5
Details: CRYSTALS WERE GROWN FROM 20% POLYETHYLENE GLYCOL 6000, 20% ISOPROPANOL, 50MM TRIS-HCL PH 7.5
Crystal
*PLUS
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein11
220 %PEG600011
320 %isopropanol11
450 mMTris-HCl11

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Data collection

DiffractionAmbient pressure: 101 kPa / Mean temperature: 100 K
Diffraction sourceSource: rotating-anode X-ray tube / Type: RIGAKU / Wavelength: 1.5418 / Target: Cu
DetectorType: IMAGE PLATE / Detector: IMAGE PLATE / Details: Rigaku R-AXIS IIc
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray / Wavelength: 1.5418 Å
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→55 Å / Num. obs: 47089 / % possible obs: 99.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 33.46 Å2 / Rmerge(I) obs: 0.04
Reflection shellHighest resolution: 2.5 Å / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 2
Reflection
*PLUS
% possible obs: 91 % / Rmerge(I) obs: 0.07

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Processing

Software
NameClassification
TNTrefinement
REFMACrefinement
XDSdata reduction
XDSdata scaling
TNTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CYS-FREE VERSION OF T4-LYSOZYME

Resolution: 2.5→55 Å / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
Details: GROUPED OCCUPANCY REFINEMENT ONLY FOR RESIDUES A39-A43 AND B34-B39. THE DENSITY FOR THESE REGIONS SUGGESTED MULTIPLE CONFORMATIONS
RfactorNum. reflection% reflection
Rwork0.227 --
all-13295 -
obs-13295 99.5 %
Solvent computationSolvent model: BABENET SCALING / Bsol: 150 Å2 / ksol: 0.8 e/Å3
Refinement stepCycle: LAST / Resolution: 2.5→55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2744 0 0 98 2842
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01127840.8
X-RAY DIFFRACTIONt_angle_deg2.137421.3
X-RAY DIFFRACTIONt_dihedral_angle_d18.417120
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes0.014005
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd0.106
Software
*PLUS
Name: TNT / Version: 5F / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.227
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_bond_d0.011
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg18.40
X-RAY DIFFRACTIONt_plane_restr0.015

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