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- PDB-3jr6: Sequential reorganization of beta-sheet topology by insertion of ... -

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Basic information

Entry
Database: PDB / ID: 3jr6
TitleSequential reorganization of beta-sheet topology by insertion of a single strand
ComponentsLysozyme
KeywordsHYDROLASE / sequence duplication / protein design / tandem repeat / beta-sheet / Antimicrobial / Bacteriolytic enzyme / Glycosidase
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 / Lysozyme domain superfamily / Phage lysozyme / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSagermann, M. / Baas, W.A. / Matthews, B.W.
Citation
Journal: Protein Sci. / Year: 2006
Title: Sequential reorganization of beta-sheet topology by insertion of a single strand.
Authors: Sagermann, M. / Baase, W.A. / Matthews, B.W.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Long-distance conformational changes in a protein engineered by modulated sequence duplication.
Authors: Sagermann, M. / Gay, L. / Matthews, B.W.
#2: 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.
History
DepositionSep 8, 2009Deposition site: RCSB / Processing site: RCSB
SupersessionOct 20, 2009ID: 2B7W
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 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 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.4Apr 3, 2024Group: Refinement description / Category: 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
C: Lysozyme
D: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,64912
Polymers76,8804
Non-polymers7698
Water0
1
A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4123
Polymers19,2201
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4123
Polymers19,2201
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4123
Polymers19,2201
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4123
Polymers19,2201
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.227, 75.915, 81.547
Angle α, β, γ (deg.)90.00, 94.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Lysozyme / / Lysis protein / Muramidase / Endolysin


Mass: 19220.088 Da / Num. of mol.: 4
Mutation: C54T, C97A, insertion of seuqence (gighll) after residue L33
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: E / Plasmid: phs 1403 / Production host: Escherichia coli (E. coli) / References: UniProt: P00720, lysozyme
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4

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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: 2.38 Å3/Da / Density % sol: 48.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 3400, 50 mM ammonium sulfate, Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Sep 5, 1998 / Details: yale mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3→32.44 Å / Num. obs: 17925 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rsym value: 0.07
Reflection shellHighest resolution: 3 Å / Rsym value: 0.097 / % possible all: 99.8

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Processing

Software
NameVersionClassification
XDSdata scaling
AMoREphasing
CCP4(refmac)refinement
CNSrefinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: T4 lysozyme I3P mutant

Resolution: 3→32.44 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Authors state that scaling and B-value refinement were performed with CNS using a recommended resolution range of 6.0-3.0 A resolution. As the B-values for the data set were determined to be ...Details: Authors state that scaling and B-value refinement were performed with CNS using a recommended resolution range of 6.0-3.0 A resolution. As the B-values for the data set were determined to be low (even for higher low-resolution cut-offs), the B-values for the atoms remained similarly low as well. Molecules A and B exhibit well-defined density of the loops. The corresponding loops of molecules B and C were in poor density but could clearly be identified. Loops and terminal residues that could not be refined reliably were omitted: B(L170), D(L170), B(34-46), C(36-46).
RfactorNum. reflection% reflectionSelection details
Rfree0.32 1279 -random
Rwork0.25 ---
all0.261 14596 --
obs0.261 14090 96.5 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.348 Å20 Å2-1.314 Å2
2---1.901 Å20 Å2
3----1.447 Å2
Refinement stepCycle: LAST / Resolution: 3→32.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5212 0 40 0 5252
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d0.0196
X-RAY DIFFRACTIONc_angle_deg2.285

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