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- PDB-1jqu: Are Carboxy Terminii of Helices Coded by the Local Sequence or by... -

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Basic information

Entry
Database: PDB / ID: 1jqu
TitleAre Carboxy Terminii of Helices Coded by the Local Sequence or by Tertiary Structure Contacts
ComponentsLysozyme
KeywordsHYDROLASE / glycine 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
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 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
DepositionAug 8, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 26, 2014Group: Database references
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software
Revision 1.5Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name
Revision 1.6Oct 27, 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 1.7Aug 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

Downloads & links

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Assembly

Deposited unit
A: Lysozyme
B: Lysozyme
C: Lysozyme
D: Lysozyme


Theoretical massNumber of molelcules
Total (without water)74,2214
Polymers74,2214
Non-polymers00
Water52229
1
A: Lysozyme


Theoretical massNumber of molelcules
Total (without water)18,5551
Polymers18,5551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysozyme


Theoretical massNumber of molelcules
Total (without water)18,5551
Polymers18,5551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Lysozyme


Theoretical massNumber of molelcules
Total (without water)18,5551
Polymers18,5551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Lysozyme


Theoretical massNumber of molelcules
Total (without water)18,5551
Polymers18,5551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.300, 77.200, 138.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Lysozyme / LYSIS PROTEIN


Mass: 18555.312 Da / Num. of mol.: 4 / Mutation: C54T, C97A, W158L
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 53.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.75
Details: 30% PEG4000, PIPES buffer ph7.0, 0.2M LiSO4, pH 6.75, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 mg/mlprotein1drop
220 mMHEPES1droppH7.0
330 %PEG40001reservoir
40.1 MPIPES1reservoirpH7.0
50.2 M1reservoirLi2SO4

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Nov 14, 1995
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→34.9 Å / Num. all: 22095 / Num. obs: 22095 / % possible obs: 79 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.42 % / Biso Wilson estimate: 36 Å2 / Rsym value: 0.057 / Net I/σ(I): 6.9
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 1.2 / Num. unique all: 3983 / Rsym value: 0.257 / % possible all: 71.5
Reflection
*PLUS
% possible obs: 78 % / Rmerge(I) obs: 0.057

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Processing

Software
NameClassification
TNTrefinement
CNSrefinement
CNSphasing
TNTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: T4 Lysozyme 2LZM

2lzm


Resolution: 2.6→35 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Molecular replacement (direct rotation searches) was carried out with lysozyme search molecules with different hinge bending-angles. The starting model was subjected to several rounds of CNS ...Details: Molecular replacement (direct rotation searches) was carried out with lysozyme search molecules with different hinge bending-angles. The starting model was subjected to several rounds of CNS SA-refinement and subsequently refined with TNT. Positve density was observed around crystal contact sites. These features, presumably PEG molecules, could not be modeled unambigously and were therefore omitted from the final model.
RfactorNum. reflectionSelection details
Rfree0.316 1616 Random
Rwork0.229 --
all0.241 20506 -
obs0.241 20506 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.18 Å20 Å20 Å2
2--2.86 Å20 Å2
3----1.68 Å2
Refinement stepCycle: LAST / Resolution: 2.6→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5212 0 0 29 5241
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.024
X-RAY DIFFRACTIONt_angle_deg2.37
Refinement
*PLUS
Highest resolution: 2.6 Å / σ(F): 0 / Rfactor all: 0.241 / Rfactor obs: 0.235 / Rfactor Rfree: 0.315
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.022
X-RAY DIFFRACTIONt_angle_deg2.2

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