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- PDB-1qqy: X-RAY CRYSTAL STRUCTURE ANALYSIS OF CANINE MILK LYSOZYME (APO-TYPE) -

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Basic information

Entry
Database: PDB / ID: 1qqy
TitleX-RAY CRYSTAL STRUCTURE ANALYSIS OF CANINE MILK LYSOZYME (APO-TYPE)
ComponentsLYSOZYME C
KeywordsHYDROLASE / APO-TYPE PROTEIN / CALCIUM BINDING LYSOZYME / ENZYME
Function / homology
Function and homology information


lysozyme / lysozyme activity / killing of cells of another organism / defense response to bacterium / metal ion binding
Similarity search - Function
Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily ...Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Lysozyme C, milk isozyme
Similarity search - Component
Biological speciesCanis lupus familiaris (dog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsKoshiba, T. / Yao, M. / Tanaka, I. / Nitta, K.
Citation
Journal: Biochemistry / Year: 2000
Title: Structure and thermodynamics of the extraordinarily stable molten globule state of canine milk lysozyme.
Authors: Koshiba, T. / Yao, M. / Kobashigawa, Y. / Demura, M. / Nakagawa, A. / Tanaka, I. / Kuwajima, K. / Nitta, K.
#1: Journal: Protein Eng. / Year: 1999
Title: Expression of a synthetic gene encoding canine milk lysozyme in Escherichia coli and characterization of the expressed protein
Authors: Koshiba, T. / Hayashi, T. / Miwako, I. / Kumagai, I. / Ikura, T. / Kawano, K. / Nitta, K. / Kuwajima, K.
History
DepositionJun 9, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LYSOZYME C


Theoretical massNumber of molelcules
Total (without water)14,6221
Polymers14,6221
Non-polymers00
Water1,45981
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.577, 68.577, 107.063
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein LYSOZYME C


Mass: 14621.643 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Species: Canis lupus / Strain: familiaris / Plasmid: PLASMID PSCREEN 1-B(+) / Production host: Escherichia coli (E. coli) / References: UniProt: P81708, lysozyme
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.5 Å3/Da / Density % sol: 51.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 4000, tri-sodium citrate, ammonium acetate, EDTA, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
20.2 Mammonium acetate1drop
330 %(w/v)PEG40001drop
41 mMEDTA1drop
50.1 Mtrisodium citrate1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Nov 25, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→100 Å / Num. obs: 13034 / % possible obs: 94.8 % / Observed criterion σ(I): 1 / Redundancy: 15.3 % / Biso Wilson estimate: 27.6 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.9
Reflection shellResolution: 1.85→1.89 Å / Rmerge(I) obs: 0.25 / Num. unique all: 725 / % possible all: 82.2
Reflection
*PLUS
Num. measured all: 199512
Reflection shell
*PLUS
% possible obs: 82.2 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EQL

1eql


Resolution: 1.85→8 Å / Rfactor Rfree error: 0.006 / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.215 1232 10 %RANDOM
Rwork0.178 ---
all-13025 --
obs-12450 95.1 %-
Solvent computationSolvent model: THROUGHOUT / Bsol: 62.4 Å2 / ksol: 0.449 e/Å3
Displacement parametersBiso mean: 26.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.565 Å21.235 Å20 Å2
2--2.565 Å20 Å2
3----5.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-8 Å
Refinement stepCycle: LAST / Resolution: 1.85→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1018 0 0 81 1099
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.414
X-RAY DIFFRACTIONc_mcbond_it1.347
X-RAY DIFFRACTIONc_mcangle_it2.294
X-RAY DIFFRACTIONc_scbond_it1.854
X-RAY DIFFRACTIONc_scangle_it2.849
LS refinement shellResolution: 1.85→1.88 Å / Rfactor Rfree error: 0.043 / Total num. of bins used: 24
RfactorNum. reflection% reflection
Rfree0.225 35 8.1 %
Rwork0.21 397 -
obs--90.64 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.007

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