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- PDB-1c7p: CRYSTAL STRUCTURE OF MUTANT HUMAN LYSOZYME WITH FOUR EXTRA RESIDU... -

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Basic information

Entry
Database: PDB / ID: 1c7p
TitleCRYSTAL STRUCTURE OF MUTANT HUMAN LYSOZYME WITH FOUR EXTRA RESIDUES (EAEA) AT THE N-TERMINAL
ComponentsLYSOZYME
KeywordsHYDROLASE / EXTRA N-TERMINAL RESIDUES
Function / homology
Function and homology information


antimicrobial humoral response / Antimicrobial peptides / specific granule lumen / azurophil granule lumen / lysozyme / lysozyme activity / tertiary granule lumen / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...antimicrobial humoral response / Antimicrobial peptides / specific granule lumen / azurophil granule lumen / lysozyme / lysozyme activity / tertiary granule lumen / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / inflammatory response / Amyloid fiber formation / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / identical protein 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsGoda, S. / Takano, K. / Yamagata, Y. / Katakura, Y. / Yutani, K.
Citation
Journal: Protein Eng. / Year: 2000
Title: Effect of extra N-terminal residues on the stability and folding of human lysozyme expressed in Pichia pastoris.
Authors: Goda, S. / Takano, K. / Yamagata, Y. / Katakura, Y. / Yutani, K.
#1: Journal: Eur.J.Biochem. / Year: 1999
Title: Effect of Foreign N-terminal Residues on the Conformational Stability of Human Lysozyme
Authors: Takano, K. / Tsuchimori, K. / Yamagata, Y. / Yutani, K.
History
DepositionFeb 29, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Nov 13, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1904
Polymers15,1211
Non-polymers693
Water3,117173
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.08, 91.08, 92.73
Angle α, β, γ (deg.)90, 90, 120
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein LYSOZYME


Mass: 15121.078 Da / Num. of mol.: 1 / Mutation: T15E, V16A, Q17E, G18A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Pichia pastoris (fungus) / References: UniProt: P61626, lysozyme
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 3.67 Å3/Da / Density % sol: 66.49 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: cadmium chloride, sodium acetate, PEG 400, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Crystal grow
*PLUS
Temperature: 10 ℃
Details: equal volume of protein and reservoir solution were used for the drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
20.1 Mcadmium chloride1reservoir
30.1 Msodium acetate1reservoir
430 %(v/v)PEG4001reservoir

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Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Dec 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionHighest resolution: 2.4 Å / Num. all: 72761 / Num. obs: 9367 / % possible obs: 99.9 % / Rmerge(I) obs: 0.044
Reflection
*PLUS
Num. measured all: 72761

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Processing

Software
NameClassification
DENZOdata reduction
AMoREphasing
X-PLORrefinement
RefinementResolution: 2.4→5 Å /
RfactorNum. reflection% reflection
obs0.197 8054 98.1 %
Refinement stepCycle: LAST / Resolution: 2.4→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1048 0 3 173 1224
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_deg1.648

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