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- PDB-176l: PROTEIN FLEXIBILITY AND ADAPTABILITY SEEN IN 25 CRYSTAL FORMS OF ... -

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Basic information

Entry
Database: PDB / ID: 176l
TitlePROTEIN FLEXIBILITY AND ADAPTABILITY SEEN IN 25 CRYSTAL FORMS OF T4 LYSOZYME
ComponentsT4 LYSOZYME
KeywordsHYDROLASE (O-GLYCOSYL)
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: 2.2 Å
AuthorsZhang, X.-J. / Weaver, L. / Dubose, R. / 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 1.0Jul 10, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 25, 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 1.4Jul 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_radiation.monochromator / _diffrn_radiation.pdbx_diffrn_protocol / _diffrn_radiation.pdbx_monochromatic_or_laue_m_l / _diffrn_radiation.pdbx_wavelength_list / _pdbx_database_status.status_code_sf / _struct_ref_seq_dif.details
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: T4 LYSOZYME
B: T4 LYSOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2423
Polymers37,2062
Non-polymers351
Water45025
1
A: T4 LYSOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6392
Polymers18,6031
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: T4 LYSOZYME


Theoretical massNumber of molelcules
Total (without water)18,6031
Polymers18,6031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.600, 127.100, 29.100
Angle α, β, γ (deg.)90.00, 98.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein T4 LYSOZYME


Mass: 18603.229 Da / Num. of mol.: 2
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 / References: UniProt: P00720, lysozyme
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.44 Å3/Da / Density % sol: 49.56 %
Crystal
*PLUS
Density % sol: 51 %
Crystal grow
*PLUS
pH: 5.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
130 %(w/v)PEG40001reservoir
20.19 M1reservoirNH4OAc
30.1 Mcitrate1reservoir

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Data collection

DiffractionAmbient pressure: 101 kPa / Mean temperature: 298 K
Diffraction sourceSource: rotating-anode X-ray tube / Type: RIGAKU RU200 / Target: Cu
DetectorType: AREA DETECTOR / Detector: AREA DETECTOR / Details: Xuong-Hamlin
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray / Wavelength: 1.5418 Å
Radiation wavelengthRelative weight: 1

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Processing

Software
NameClassification
TNTrefinement
Xengen (HOWARD, NIELSEN, XUONG)data scaling
RefinementResolution: 2.2→14 Å / Rfactor obs: 0.183
Refinement stepCycle: LAST / Resolution: 2.2→14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2614 0 1 25 2640
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.015
X-RAY DIFFRACTIONt_angle_deg2.3
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

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