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- PDB-3cdo: Bacteriophage T4 lysozyme mutant R96V in wildtype background at l... -

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Basic information

Entry
Database: PDB / ID: 3cdo
TitleBacteriophage T4 lysozyme mutant R96V in wildtype background at low temperature
ComponentsLysozyme
KeywordsHYDROLASE / BACTERIOPHAGE T4 LYSOZYME / VIRAL LYSOZYME / MUTATIONAL ANALYSIS / PROTEIN ENGINEERING / THERMAL STABILITY / PROTEIN STABILITY / PROTEIN ELECTROSTATICS / PROTEIN STRUCTURE / CHARGE BURIAL / HYDROGEN BONDING / HELIX DIPOLE / PROTEIN CREVICES / STERIC STRAIN / TEMPERATURE-SENSITIVE MUTANT / PHOSPHATE BINDING SITE / MPD BINDING SITE / CHLORIDE BINDING SITE / 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 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HEXANE-1,6-DIOL / Endolysin
Similarity search - Component
Biological speciesBacteriophage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsMooers, B.H.M.
Citation
Journal: Protein Sci. / Year: 2009
Title: Contributions of all 20 amino acids at site 96 to the stability and structure of T4 lysozyme.
Authors: Mooers, B.H. / Baase, W.A. / Wray, J.W. / Matthews, B.W.
#1: Journal: Protein Sci. / Year: 2009
Title: Evaluation at atomic resolution of the role of strain in destabilizing the temperature-sensitive T4 lysozyme mutant Arg 96 --> His.
Authors: Mooers, B.H. / Tronrud, D.E. / Matthews, B.W.
History
DepositionFeb 27, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 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 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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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)75,93918
Polymers74,4184
Non-polymers1,52214
Water14,250791
1
A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9594
Polymers18,6041
Non-polymers3553
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8934
Polymers18,6041
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9374
Polymers18,6041
Non-polymers3323
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1516
Polymers18,6041
Non-polymers5475
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.820, 99.316, 123.012
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51A
61B
71C
81D

NCS domain segments:

Ens-ID: 1 / Refine code: 6

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETTYRTYRAA1 - 181 - 18
21METMETTYRTYRBB1 - 181 - 18
31METMETTYRTYRCC1 - 181 - 18
41METMETTYRTYRDD1 - 181 - 18
52LEULEULYSLYSAA32 - 16232 - 162
62LEULEULYSLYSBB32 - 16232 - 162
72LEULEULYSLYSCC32 - 16232 - 162
82LEULEULYSLYSDD32 - 16232 - 162

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Components

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


Mass: 18604.404 Da / Num. of mol.: 4 / Mutation: R96V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteriophage T4 (virus) / Gene: E / Plasmid: PHS1403 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): RR1 / References: UniProt: P00720, lysozyme
#2: Chemical
ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 791 / 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: 2.37 Å3/Da / Density % sol: 48.16 %
Crystal growpH: 6
Details: 100 MM MES, 200 MM LITHIUM SULFATE, 35% MPD, 50 MM 1,6-HEXANEDIOL, 12.5 MG/ML, PH 6.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K, pH 6.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.07
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 15, 2001
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 1.87→23.881 Å / Num. obs: 58798 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 10.5
Reflection shellResolution: 1.87→1.97 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.235 / % possible all: 95.5

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Processing

Software
NameVersionClassification
EPMRphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L63

1l63


Resolution: 1.87→23.82 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.913 / SU B: 3.331 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1134 1.9 %RANDOM
Rwork0.187 ---
obs0.187 57595 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.477 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.87→23.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5310 0 62 859 6231
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225459
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1121.977354
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7095675
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.57623.509265
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.662151063
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4091556
X-RAY DIFFRACTIONr_chiral_restr0.0720.2816
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024006
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1920.22790
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.23799
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2616
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.2117
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.260
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5851.53401
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.95625288
X-RAY DIFFRACTIONr_scbond_it1.66832364
X-RAY DIFFRACTIONr_scangle_it2.6324.52066
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 1076 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Aloose positional0.425
2Bloose positional0.485
3Cloose positional0.425
4Dloose positional0.455
1Aloose thermal1.9310
2Bloose thermal2.8310
3Cloose thermal2.5210
4Dloose thermal3.210
LS refinement shellResolution: 1.87→1.92 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 62 -
Rwork0.218 3882 -
obs--91.72 %

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