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- PDB-1el1: X-RAY CRYSTAL STRUCTURE ANALYSIS OF CANINE MILK LYSOZYME (HOLO-TYPE) -

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Basic information

Entry
Database: PDB / ID: 1el1
TitleX-RAY CRYSTAL STRUCTURE ANALYSIS OF CANINE MILK LYSOZYME (HOLO-TYPE)
ComponentsLYSOZYME C
KeywordsHYDROLASE / Calcium binding lysozyme / Holo-form / C-type lysozyme
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 / Resolution: 1.9 Å
AuthorsKoshiba, T. / Yao, M. / Tanaka, I. / Nitta, K.
Citation
Journal: To be Published
Title: Calcium Induced Conformational Changes of Canine Milk Lysozyme Revealed by Structural and Thermodynamical Evidences
Authors: Koshiba, T. / Yao, M. / Tanaka, I. / Nitta, K.
#1: 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.
#2: 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
DepositionMar 13, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: LYSOZYME C
B: LYSOZYME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2354
Polymers29,1552
Non-polymers802
Water2,522140
1
A: LYSOZYME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6182
Polymers14,5781
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LYSOZYME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6182
Polymers14,5781
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.3, 31.3, 202.5
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein LYSOZYME C


Mass: 14577.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Species: Canis lupus / Strain: familiaris / Plasmid: PSCREEN 1-B(+) / Production host: Escherichia coli (E. coli) / References: UniProt: P81708, lysozyme
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 1.96 Å3/Da / Density % sol: 37.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: ammonium sulfate, sodium phosphate, calcium chloride, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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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: Jan 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→100 Å / Num. obs: 16169 / % possible obs: 91.9 % / Observed criterion σ(I): 0 / Redundancy: 2.66 % / Biso Wilson estimate: 32.7 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 11.2
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.29 / Num. unique all: 1423 / % possible all: 90.7

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementResolution: 1.9→10 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1404 -RANDOM
Rwork0.159 ---
all-17398 --
obs-15524 89.2 %-
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2032 0 2 140 2174
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.33804
X-RAY DIFFRACTIONc_bond_d0.006375

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