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- PDB-1llh: ARE CARBOXY TERMINII OF HELICES CODED BY THE LOCAL SEQUENCE OR BY... -

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Basic information

Entry
Database: PDB / ID: 1llh
TitleARE CARBOXY TERMINII OF HELICES CODED BY THE LOCAL SEQUENCE OR BY TERTIARY STRUCTURE CONTACTS
ComponentsLysozyme
KeywordsHYDROLASE / helix terminii / schellman motif / alpha-l motif
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
BETA-MERCAPTOETHANOL / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / Isomorphous replacement / Resolution: 1.8 Å
AuthorsSagermann, M. / Martensson, L.-G. / Baase, W.A. / Matthews, B.W.
Citation
Journal: Protein Sci. / Year: 2002
Title: A test of proposed rules for helix capping: Implications for protein design
Authors: Sagermann, M. / Martensson, L.-G. / Baase, W.A. / Matthews, B.W.
#1: Journal: Science / Year: 1994
Title: Rules for alpha-helix termination by glycine.
Authors: Aurora, R. / Srinivasan, R. / Rose, G.D.
#2: Journal: Protein Folding / Year: 1980
Title: The alpha-L Conformations at the Ends of Helices
Authors: Schellman, C.
#3: Journal: J.Mol.Biol. / Year: 1987
Title: Structure of bacteriophage T4 lysozyme refined at 1.7 A resolution.
Authors: Weaver, L.H. / Matthews, B.W.
History
DepositionApr 28, 2002Deposition site: RCSB / Processing site: RCSB
SupersessionMay 15, 2002ID: 1JOZ
Revision 1.0May 15, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 26, 2014Group: Database references
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software
Revision 1.5Jul 22, 2020Group: Data collection / Other / Refinement description
Category: diffrn / diffrn_detector ...diffrn / diffrn_detector / diffrn_radiation / diffrn_source / pdbx_database_status / software
Item: _diffrn.ambient_pressure / _diffrn_detector.details ..._diffrn.ambient_pressure / _diffrn_detector.details / _diffrn_detector.type / _diffrn_radiation.monochromator / _diffrn_radiation.pdbx_wavelength_list / _diffrn_source.source / _diffrn_source.target / _pdbx_database_status.status_code_sf
Revision 1.6Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.7Aug 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

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Assembly

Deposited unit
A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7894
Polymers18,6401
Non-polymers1493
Water1,06359
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.977, 60.977, 97.386
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


Mass: 18640.418 Da / Num. of mol.: 1 / Mutation: C54T, C97A, T157I
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 / Gene: E / Plasmid: pHS1403 / Production host: Escherichia coli (E. coli) / Strain (production host): RR1 / References: UniProt: P00720, lysozyme
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.8 Å3/Da / Density % sol: 56.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 1.8M Phosphate, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionAmbient pressure: 101 kPa / Mean temperature: 298 K
Diffraction sourceSource: rotating-anode X-ray tube / Type: RIGAKU RU200 / Wavelength: 1.5418 Å / Target: Cu
DetectorType: AREA DETECTOR / Detector: AREA DETECTOR / Date: Feb 15, 1995 / Details: Xuong-Hamlin
RadiationMonochromator: graphite / 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: 1.8→26.44 Å / Num. all: 17775 / Num. obs: 17775 / % possible obs: 81 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.37 % / Biso Wilson estimate: 16.36 Å2 / Rsym value: 0.04 / Net I/σ(I): 10.76
Reflection shellResolution: 1.8→1.94 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.215 / Mean I/σ(I) obs: 1.9 / Num. unique all: 3101 / % possible all: 81

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Processing

Software
NameClassification
TNTrefinement
Xengen (HOWARD, NIELSEN, XUONG)data scaling
RefinementMethod to determine structure: Isomorphous replacement
Starting model: PDB entry 2LZM

2lzm


Resolution: 1.8→27 Å / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Residues 163 and 164 are missing in the electron density.
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1388 -RANDOM
Rwork0.192 ---
all0.2 17775 --
obs0.2 17775 79 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.26 Å20.26 Å20 Å2
2--0.26 Å20 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 1.8→27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1293 0 6 59 1358
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.011
X-RAY DIFFRACTIONt_angle_deg1.527

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