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- PDB-3mgw: Thermodynamics and structure of a salmon cold-active goose-type l... -

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Basic information

Entry
Database: PDB / ID: 3mgw
TitleThermodynamics and structure of a salmon cold-active goose-type lysozyme
ComponentsLysozyme g
KeywordsHYDROLASE / Salmon / goose-type / lysozyme / differential scanning calorimetry / refolding / thermal tolerance / innate immunity
Function / homology
Function and homology information


peptidoglycan catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-positive bacterium / extracellular region
Similarity search - Function
Glycoside hydrolase, family 23 / Transglycosylase SLT domain 1 / Transglycosylase SLT domain / Lysozyme - #10 / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSalmo salar (Atlantic salmon)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsKyomuhendo, P. / Myrnes, B. / Brandsdal, B.O. / Smalas, A.O. / Nilsen, I.W. / Helland, R.
CitationJournal: Comp.Biochem.Physiol. B: Biochem.Mol.Biol. / Year: 2010
Title: Thermodynamics and structure of a salmon cold active goose-type lysozyme
Authors: Kyomuhendo, P. / Myrnes, B. / Brandsdal, B.O. / Smalas, A.O. / Nilsen, I.W. / Helland, R.
History
DepositionApr 7, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2014Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme g
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4283
Polymers20,2731
Non-polymers1552
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)103.15, 103.15, 48.67
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Lysozyme g / Goose-type lysozyme


Mass: 20272.795 Da / Num. of mol.: 1 / Fragment: g-type lysozyme, UNP residues 22-200
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmo salar (Atlantic salmon) / Gene: lysG, LYG / Plasmid: pQE-2 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 (pREP4) / References: UniProt: A6PZ97, lysozyme
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHOR STATED THAT RESIDUE A133V WAS NOT A INTENTIONAL MUTATION, MAYBE AN EXPRESSION ARTIFACT.

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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: 2.46 Å3/Da / Density % sol: 49.96 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 43-45 % ammonium sulphate, 0.01M cobalt chloride, 0.1M MES , pH 6.25-6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
PH range: 6.25-6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 4, 2007
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.75→42.76 Å / Num. all: 19410 / Num. obs: 19410 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 20.38 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 11.3
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.5 / Num. unique all: 2840 / Rsym value: 0.49 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MAR345CCDdata collection
MOLREPphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 153L

153l


Resolution: 1.75→42.76 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.379 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; 2. The polypeptide is traced where electron density is observed, but density for residues 22-24 indicates disorder. There appears to be ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; 2. The polypeptide is traced where electron density is observed, but density for residues 22-24 indicates disorder. There appears to be proteolytic cleavage after residue 21.
RfactorNum. reflection% reflectionSelection details
Rfree0.215 989 5.1 %RANDOM
Rwork0.176 ---
obs0.178 18417 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.55 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å2-0.12 Å20 Å2
2---0.23 Å20 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.75→42.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1429 0 6 148 1583
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211479
X-RAY DIFFRACTIONr_angle_refined_deg1.2981.9291993
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3535183
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.82123.52171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.59615263
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.1741511
X-RAY DIFFRACTIONr_chiral_restr0.0910.2208
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021127
X-RAY DIFFRACTIONr_nbd_refined0.2070.2738
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21007
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2110
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1230.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2160.215
X-RAY DIFFRACTIONr_mcbond_it0.9871.5928
X-RAY DIFFRACTIONr_mcangle_it1.58121439
X-RAY DIFFRACTIONr_scbond_it2.3683633
X-RAY DIFFRACTIONr_scangle_it3.5844.5554
LS refinement shellResolution: 1.75→1.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 87 -
Rwork0.249 1351 -
obs--100 %

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