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- PDB-1lz6: STRUCTURAL AND FUNCTIONAL ANALYSES OF THE ARG-GLY-ASP SEQUENCE IN... -

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Basic information

Entry
Database: PDB / ID: 1lz6
TitleSTRUCTURAL AND FUNCTIONAL ANALYSES OF THE ARG-GLY-ASP SEQUENCE INTRODUCED INTO HUMAN LYSOZYME
ComponentsHUMAN LYSOZYME
KeywordsHYDROLASE(O-GLYCOSYL)
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 / Resolution: 1.8 Å
AuthorsMatsushima, M. / Inaka, K. / Yamada, T. / Sekiguchi, K. / Kikuchi, M.
Citation
Journal: J.Biol.Chem. / Year: 1993
Title: Structural and functional analyses of the Arg-Gly-Asp sequence introduced into human lysozyme.
Authors: Yamada, T. / Matsushima, M. / Inaka, K. / Ohkubo, T. / Uyeda, A. / Maeda, T. / Titani, K. / Sekiguchi, K. / Kikuchi, M.
#1: Journal: Science / Year: 1992
Title: Structure of a Fibronectin Typeiii Domain from Tenascin Phased by MAD Analysis of the Selenomethionyl Protein
Authors: Leahy, D.J. / Hendrickson, W.A. / Aukhil, I. / Erickson, H.P.
#2: Journal: J.Biol.Chem. / Year: 1991
Title: The Crystal Structure of a Mutant Human Lysozyme C77(Slash)95A with Increased Secretion Efficiency in Yeast
Authors: Inaka, K. / Taniyama, Y. / Kikuchi, M. / Morikawa, K. / Matsushima, M.
History
DepositionFeb 3, 1993Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Oct 23, 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 / 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: HUMAN LYSOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5343
Polymers15,4631
Non-polymers712
Water2,882160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.790, 60.970, 33.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HUMAN LYSOZYME


Mass: 15463.455 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P61626, lysozyme
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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

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Sample preparation

CrystalDensity Matthews: 1.88 Å3/Da / Density % sol: 34.71 %
Crystal grow
*PLUS
Temperature: 13.0 ℃ / pH: 6 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein11
23.0 M12NaCl
330 mMsodium phosphate12

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 10586 / Rmerge(I) obs: 0.056

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.8→6 Å
Details: THE ELECTRON DENSITY MAP WITHOUT THE PHASE CONTRIBUTION OF RESIDUES ALA 73, VAL 74 AND THE INSERTED AMINO ACIDS DID NOT SHOW SIGNIFICANT ELECTRON DENSITIES FOR THE RESIDUES FROM ALA 73 TO ...Details: THE ELECTRON DENSITY MAP WITHOUT THE PHASE CONTRIBUTION OF RESIDUES ALA 73, VAL 74 AND THE INSERTED AMINO ACIDS DID NOT SHOW SIGNIFICANT ELECTRON DENSITIES FOR THE RESIDUES FROM ALA 73 TO PRO 74G, BUT THE MAP CLEARLY SHOWED THE ELECTRON DENSITY OF ALA 74H. THE REFINED B FACTORS OF THE RESIDUES ALA 73 TO PRO 74G ARE LARGE WITH POORLY DEFINED POSITIONAL PARAMETERS.
RfactorNum. reflection
obs0.152 10586
Refinement stepCycle: LAST / Resolution: 1.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1081 0 2 160 1243
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.014
X-RAY DIFFRACTIONp_angle_d0.0370.037
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 6 Å / Num. reflection obs: 10586 / Rfactor obs: 0.152
Solvent computation
*PLUS
Displacement parameters
*PLUS

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