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- PDB-180l: PROTEIN FLEXIBILITY AND ADAPTABILITY SEEN IN 25 CRYSTAL FORMS OF ... -

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Basic information

Entry
Database: PDB / ID: 180l
TitlePROTEIN FLEXIBILITY AND ADAPTABILITY SEEN IN 25 CRYSTAL FORMS OF T4 LYSOZYME
ComponentsLYSOZYME
KeywordsCOMPLEX (HYDROLASE/CELL WALL) / COMPLEX (HYDROLASE-CELL WALL) / COMPLEX (HYDROLASE-CELL WALL) complex
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 / Resolution: 1.75 Å
AuthorsKuroki, R. / Weaver, L. / Zhang, X.-J. / Matthews, B.W.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: Protein flexibility and adaptability seen in 25 crystal forms of T4 lysozyme.
Authors: Zhang, X.J. / Wozniak, J.A. / Matthews, B.W.
#1: Journal: J.Mol.Biol. / Year: 1987
Title: Structure of Bacteriophage T4 Lysozyme Refined at 1.7 Angstroms Resolution
Authors: Weaver, L.H. / Matthews, B.W.
History
DepositionMar 24, 1995Processing site: BNL
Revision 1.0Apr 3, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)37,3132
Polymers37,3132
Non-polymers00
Water1,38777
1
A: LYSOZYME


Theoretical massNumber of molelcules
Total (without water)18,6561
Polymers18,6561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LYSOZYME


Theoretical massNumber of molelcules
Total (without water)18,6561
Polymers18,6561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.300, 57.700, 57.600
Angle α, β, γ (deg.)90.00, 104.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein LYSOZYME


Mass: 18656.373 Da / Num. of mol.: 2 / Mutation: T26E, C54T, C97A
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: M13 / Production host: Escherichia coli (E. coli) / References: UniProt: P00720, lysozyme
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.47 %
Crystal
*PLUS
Density % sol: 47 %
Crystal grow
*PLUS
pH: 7.5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
124 %(w/v)PEG40001reservoir
20.25 M1reservoirNaCl
30.05 Mphosphate1reservoir
450 mMbeta-mercaptoethanol1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 1.75→30 Å / σ(F): 0
Details: MUTANT SPACE GROUP, P 2(1), IS NON-ISOMORPHOUS TO WILD TYPE. STARTING COORDINATES WERE BASED ON THE MUTANT T26E WITH ADDUCTED CELL WALL FRAGMENT MODEL. RESIDUES 162 - 164 IN WILD-TYPE AND ...Details: MUTANT SPACE GROUP, P 2(1), IS NON-ISOMORPHOUS TO WILD TYPE. STARTING COORDINATES WERE BASED ON THE MUTANT T26E WITH ADDUCTED CELL WALL FRAGMENT MODEL. RESIDUES 162 - 164 IN WILD-TYPE AND ALL MUTANT LYSOZYMES ARE EXTREMELY MOBILE. THUS THE COORDINATES FOR THESE RESIDUES ARE VERY UNRELIABLE.
RfactorNum. reflection% reflection
obs0.178 28843 84 %
Refinement stepCycle: LAST / Resolution: 1.75→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2605 0 0 77 2682
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.018
X-RAY DIFFRACTIONt_angle_deg2.8
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Refinement
*PLUS
Rfactor obs: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS

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