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- PDB-1oyu: Long-Distance conformational changes in a protein engineered by m... -

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Basic information

Entry
Database: PDB / ID: 1oyu
TitleLong-Distance conformational changes in a protein engineered by modulated sequence duplication
ComponentsLysozyme
KeywordsHYDROLASE / sequence duplication / design of structural switches / tandem repeat / protein design
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSagermann, M. / Gay, L. / Matthews, B.W.
Citation
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.
#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.
History
DepositionApr 7, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Advisory / Data collection / Refinement description / Category: pdbx_unobs_or_zero_occ_residues / software / Item: _software.classification / _software.name
Revision 1.4Aug 14, 2019Group: Data collection / Category: computing
Revision 1.5Oct 27, 2021Group: Advisory / Database references
Category: database_2 / pdbx_unobs_or_zero_occ_residues / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Aug 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


Theoretical massNumber of molelcules
Total (without water)39,0272
Polymers39,0272
Non-polymers00
Water2,198122
1
A: Lysozyme


Theoretical massNumber of molelcules
Total (without water)19,5131
Polymers19,5131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysozyme


Theoretical massNumber of molelcules
Total (without water)19,5131
Polymers19,5131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.350, 60.350, 213.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsTwo molecules in the asymmetric unit, A and B, refinement was carried out in the absence of NCS relationship

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Components

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


Mass: 19513.361 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: phs1403 / Production host: Escherichia coli (E. coli) / Strain (production host): RR1 / References: UniProt: P00720, lysozyme
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.49 Å3/Da / Density % sol: 50.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 25% poly-ethylene glycol 4000, 50mM phosphate buffer, 0.2mM ammonium acetate, 20% isopropanol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
125 %(w/v)PEG40001reservoir
220 %(v/v)isopropanol1reservoir
350 mMphosphate buffer1reservoirpH5.5
40.2 mMammonium acetate1reservoir

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Data collection

DiffractionMean temperature: 170 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.99 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 10, 2001 / Details: mirrors
RadiationMonochromator: Flat mirror, single SI crystal bend / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.5→36.62 Å / Num. obs: 13538 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 43.7 Å2 / Rsym value: 0.072 / Net I/σ(I): 8.2
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 5.21 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 2047 / Rsym value: 0.22 / % possible all: 96.6
Reflection
*PLUS
Num. obs: 12441 / Rmerge(I) obs: 0.072

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Processing

Software
NameVersionClassification
TNTrefinement
SCALAdata scaling
AMoREphasing
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3lzm

3lzm


Resolution: 2.5→37 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: In molecule A, the density between residues 53-64 is very poor. The occupancy of these atoms has been set to zero. In Molecule B, the density for the main chain was clearly visible in OMIT ...Details: In molecule A, the density between residues 53-64 is very poor. The occupancy of these atoms has been set to zero. In Molecule B, the density for the main chain was clearly visible in OMIT maps, however, the density is weak and no side chain density could be identified. After several trials of refinement, the occupancy has been set to 0.6 for atoms of residues 53-64. Also, the final amino acids Asn174 and Leu175 could not be localized in the structure.
RfactorNum. reflectionSelection details
Rfree0.324 991 RANDOM
Rwork0.209 --
obs0.219 12441 -
all-12441 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.31 Å20 Å20 Å2
2---0.31 Å20 Å2
3---0.62 Å2
Refinement stepCycle: LAST / Resolution: 2.5→37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2658 0 0 122 2780
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.01
X-RAY DIFFRACTIONt_angle_deg1.647
X-RAY DIFFRACTIONt_dihedral_angle_d15.975
Software
*PLUS
Name: CNS / Version: 1.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d

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