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- PDB-1jtn: Alternative Structures of a Sequence Extended T4 Lysozyme Show th... -

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Basic information

Entry
Database: PDB / ID: 1jtn
TitleAlternative Structures of a Sequence Extended T4 Lysozyme Show that the Highly Conserved Beta-Sheet Region has weak intrinsic Folding Propensity
ComponentsLYSOZYME
KeywordsHYDROLASE / SEQUENCE DUPLICATION / CONTEXT DEPENDENT FOLDING / SEQUENCE REPEAT
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSagermann, M. / Matthews, B.W.
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: Crystal Structures of a T4-lysozyme Duplication-extension Mutant Demonstrate that the Highly Conserved beta-Sheet Region has Low Intrinsic Folding Propensity
Authors: Sagermann, M. / Matthews, B.W.
#1: 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.
#2: 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 21, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 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 1.4Aug 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
B: LYSOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6354
Polymers40,4422
Non-polymers1922
Water2,522140
1
A: LYSOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3172
Polymers20,2211
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LYSOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3172
Polymers20,2211
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.125, 32.314, 85.925
Angle α, β, γ (deg.)90.00, 102.64, 90.00
Int Tables number4
Space group name H-MP1211
DetailsMolecules A and B in the asymmetric unit are related by an approximate translation. Refinement was carried out in the absence of an NCS relationship

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Components

#1: Protein LYSOZYME / LYSIS PROTEIN


Mass: 20221.203 Da / Num. of mol.: 2 / Mutation: 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 / Gene: E / Plasmid: phs1403 / Production host: Escherichia coli (E. coli) / Strain (production host): RR1 / References: UniProt: P00720, lysozyme
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.01 Å3/Da / Density % sol: 38.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 50m Tris-Glycine, 200mM Lisulfate, 18% PEG 4000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.5 / Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mMTris-glycine1droppH7.5
2100 mM1dropNaCl
320 mg/mlprotein1drop
418 %PEG40001reservoir
5200 mMlithium sulfate1reservoir
650 mMTris-glycine1reservoirpH6.8

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Data collection

DiffractionMean temperature: 170 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.773 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 23, 2001 / Details: mirrors
RadiationMonochromator: FLAT MIRROR, SINGLE SI CRYSTAL BEND MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.773 Å / Relative weight: 1
ReflectionResolution: 2.3→19.6 Å / Num. all: 14476 / Num. obs: 14476 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 27 Å2 / Rsym value: 4.4 / Net I/σ(I): 13.6
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 7 / Num. unique all: 2077 / Rsym value: 0.1 / % possible all: 98.9
Reflection
*PLUS
% possible obs: 97.6 % / Rmerge(I) obs: 0.043

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Processing

Software
NameVersionClassification
AMoREphasing
TNTrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 2LZM

2lzm


Resolution: 2.3→19.6 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The structural refinement was carried out with the NCS switched off since the appended peptide of both molecules packs differently for each monomer. Residual density was observed around ...Details: The structural refinement was carried out with the NCS switched off since the appended peptide of both molecules packs differently for each monomer. Residual density was observed around residues B41 and fitted with H2O molecules. These water molecules, however, do not fit the 3.5A distance criteria. The difference density is most likely caused by PEG molecules and not by the appended peptide. The last residue of molecule A and the last four residues of molecule B were not clearly identifiable in the difference maps. A refinement with the program BUSTER showed 3 remaining residues of molecule B. Their occupancy, however, refined to low values and were therefore not included in the final model. Combination of CNS, BUSTER and TNT used for refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.314 1085 -random
Rwork0.22 ---
all0.232 16264 --
obs0.232 16264 95 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.57 Å20 Å2-3.04 Å2
2--1.59 Å20 Å2
3----2.16 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2801 0 10 140 2951
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.006
X-RAY DIFFRACTIONt_angle_deg1.12
Refinement
*PLUS
Rfactor all: 0.232 / Rfactor obs: 0.221 / Rfactor Rfree: 0.314 / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_angle_deg / Dev ideal: 1.1

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